Dark Vengeance
by SirScribe
Summary: Discord. Queen Chrysalis. King Sombra. Nightmare Moon. United, they pose a great threat to Equestria, and it won't be an easy fight for the Mane 6. When Twilight finds herself alone, she must ally herself with new friends in order to take back her home. This won't be easy. Will Twilight and her new friends save Equestria and the Elements? Or will darkness reign for all eternity?
1. Enemies assemble

**A/N: Greetings bronies and pegasisters! Sir Scribe here with an actual fanfic! I must say, I am a little disappointed with my first work that I posted, but that was expected. I mean, who else reads a fic featuring nothing but an OC? *hands and hooves rise* Where the hay were you then? Oh well, at least some of you exist. Anyway, let's get this party started!**

**Pinkie: PARTY! WHOOOOO!**

**Me: Ow, PINKIE!**

**Pinkie: What? None of your Fanfiction followers or viewers can hear me**

**Me: But I can! Please tone it down a little bit**

**Pinkie: *laughs* You're funny**

**Me: I don't think so. Anyway, care to do the honors?**

**Pinkie: Certainly. Sir Scribe doesn't own My Little Pony: Friendship is Magic. All rights and characters belong to Hasbro Studios and Lauren Faust.**

**Me: Fillies and Gentlecolts, I hearby present to you- DARK VENGEANCE!**

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><p>3rd POV:<p>

Thunder and lightning dominated the Canterlot night. With the storm passing over the Everfree Forest and parts of the desert, most ponies really had a reason to remain indoors for the night. The scheduled Galaxy Watch, the newest event hosted by Princess Luna, just had to wait until the storm passed. Little did everypony know, that a bigger storm was headed their way. A storm unlike any before it.

In the darkened alleyways of Canterlot, a group of individuals met. Judging by the sizes of their shadows, there were three equines present. Two alicorns and one unicorn with an oddly shaped horn. The three were conversing with themselves when a slithering shadow formed next the the unicorn. "Are we all here?"

One of the alicorns nodded. "All except for the blue one. She proclaimed that she wasn't going ahead with this operation. And she actually defeated Twilight Sparkle!"

The snake-like figure nodded its misformed head. "I expected that from a friend of hers. Anyway, as long as we all are here, we can begin."

The unicorn stepped forward. "Who put you in charge of this operation? Out of all of us, I am royalty! I am to be given the right to lead us!"

"Nay, the powers of this group must be ours! We will not serve under the leadership of a failed king!" One alicorn said.

"Well as long as I am given a full pardon to perform my task, I don't care. Although, for the record, I am also royalty! I am a greater power than all of you. Plus, I have an army!" the other said.

The snake sighed. "I don't have to put up with this. I assembled you all back from your defeat in hopes that you will aid me in this. King Sombra, I was able to find your horn and bring you back from obliteration. Don't forget that. Chrysalis, let's not forget that it was I who sought you out after you were defeated!"

Chrysalis growled. "I don't care. Besides, I would've been fine without your help."

Sombra laughed. "You were thrown out of Canterlot by the power of Love. The very substance that you feed on! You're pathetic!"

"Says the unicorn who was defeated by a crystal. I was defeated by real magic! And you, Nightmare, what's your story?"

The alicorn shuffled in her place. "Elements of Harmony. Well, proper timing with a regeneration spell. I was never truly defeated!"

The snake laughed. "You were cornered by 6 ponies who barely knew eachother, tried to destroy the Elements, and just stood there while the Elements were taking their new form. If I was you, I would've put down Twilight before her Element was assembled. At least defeat somepony," the snake said.

"Oh please Discord! You befriended the enemies. How do we know you are with us?" Nightmare Moon stated.

"Because I was the one who found all of you and assembled you. I have big plans for Equestria after what happened over a thousand years ago. My empire was taken from me!"

"Mine too!" Sombra declared.

"Mine as well!" Nightmare declared.

"And my children were reduced to scavengers thanks to Celestia!" Chrysalis said.

Discord sighed. "Then we all have an understanding. The enemy is Celestia. Our weapons: the Elements and their bearers. If I understand correctly, all 6 of them parted ways for the time being. You all have your targets, yes?"

All 3 of them nodded. "Then by tomorrow night, Equestria will be ours, and Celestia will be out of the way. We will finally have our revenge."

All 4 cheered silently. Discord laughed. "We are due for a big helping of CHAOS!"

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><p>Twilight groaned as she stirred to consciousness. She raised her head off her pillow and looked around. That was hard with crusty eyes and an out of control mane. She blew the biggest clump of her mane out of her vision to see clearly. Still crusty eyes, but what are you going to do when you spent the last 3 weeks doing damage control.<p>

Word of Twilight's journey into the human world grabbed a lot of attention in Equestria. Ponies declared that the royal family had the power to cross dimensions and bring deadly creatures to their world. After a while, Cadence had to publicly report that the mirror disappeared. That calmed some tension in Equestria, but ponies were still outraged that such a secret was being kept from them. Ever since then, Twilight has had letters coming in, both good and bad. Some ponies called her brave while others claimed she was a pawn being used to detour some of the anger.

She dusted all the letters from her bed and walked over to her mirror. She had bags under her eyes. Something nopony liked seeing. She used her magic to calm her mane, but it was still wild. At least it was a bit presentable. She extended her wings to get another look at them. Ever since she was torn away from Ponyville, she kept thinking that her ordeal in the human world and her wings were just a dream. She always imagined waking up in her library without wings and everything back to normal.

She never got that fantasy.

She sighed. "Another day of training Twi. Another day with Celestia."

Suddenly, she heard a burp originate from behind her. She turned. Turns out to be only Spike. Next to him was a letter. _Princess Celestia probably,_ she thought.

She levitated the scroll to her and began to read. She had to reread the letter. It read:

_Dear Twilight Sparkle,_

_I'm afraid I will have to cancel our lessons for today. An emergency has arisen in Manehattan and I must be there for damage control. Meanwhile, I left Princess Luna in charge of the castle. Unless you want lessons from Luna, you have the day off. Go on and enjoy life beyond the castle AND library. I want you to enjoy today. The storm really brought out the beauty of Equestria._

_Enjoy,_

_-Princess Celestia_

Twilight smiled. She heard Spike groan from pain. "Who was it from?" he asked in his sleep.

"Princess Celestia. Something is happening in Manehattan and she left to take care of it. Why didn't she take Luna with her?" Twilight asked.

"Maybe Princess Luna was too tired of guarding the night," he said.

Twilight nodded. While she studied with Celestia during the day, she spent most of her nights with Luna in the Dream World. She learned how to indirectly aid ponies in their nightly endeavors. It got awkward in a few dreams over the past month, but it was something Twilight had to get used to. "Maybe you're right. Besides, today we have a day off. Wanna head out somewhere?"

Spike jumped up. "How about we go visit our friends. It's been a while since we've seen them."

Twilight chuckled. "You just want to see Rarity, don't you?"

Spike blushed. "You make it sound like I don't miss our friends."

Twilight raised an eyebrow. "Do you miss our friends?"

"Of course, but I miss Rarity more."

Twilight laughed, and left to go wash up. Spike paced in the room and began clearing his throat. After a while, Twilight reappeared and they both left Canterlot behind them. The scroll Twilight left behind began to glow, and formed the face of Discord. "Oh this is perfect. Step 1 is a go." Discord disappeared immediately, ready for the day to progress.

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><p><strong>AN: Well, I hope you liked this first chapter of Dark Vengeance. I plan on making about 21 chapters for this one. Remember to Favorite, Follow, and possibly Review to show support. I'll catch you all real soon, and Flutter On!**

**-Sir Scribe**


	2. Return to Ponyville

**A/N: You know guys, I really am trying to get through this. I guess I am a bit rusty, but at least I am trying. Anyway, back to the story. I plan on continuing this and my OC story. After that, I don't know. I am getting no response. It's like casting a line out into the lake and waiting 5 whole hours with no luck. It's impossible. To anyone who is reading this, thank you for at least browsing through this. It means a lot to know at least some people read this.**

**Pinkie: Aw, nothing to report?**

**Me: Afraid not. Got anything to help?**

**Pinkie: I got a party cannon!**

**Me: Sweet Celestia. Anyway, I don't own MLP. All rights go to Lauren Faust and Hasbro studios. Did you know that talks of an Equestria Girls 2 movie is going on?**

**Pinkie: That'll be fun!**

**Me: Leave it to Pinkie to know about a movie based around the lives of her friends. Anyway, ONWARDS!**

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><p>Twilight hated flying in the morning. The recent storm left most of Canterlot in a heavy fog. The pegasus ponies were quick to conjure up such a storm for the area, but there were talks among the unicorns of Canterlot: the storm wasn't supervised by the pegasi. Twilight immediately dismissed such an accusation. It was impossible for a storm to exist without the pegasi. Her beliefs, however, were challenged in the human world.<p>

With Spike on her back, Twilight tried to stabilize herself. "It's a bit cold up here, ya know?" Spike asked.

Twilight nodded. "The pegasi really did a good job with the storm last night. It reminds me of the storm that we had in Ponyville a few years ago," she said.

"The one I missed?"

Twilight nodded. "Also the night Applejack and Rarity slept over."

Spike facepalmed. Twilight chuckled. She never told Spike that Rarity was at their place the one night he wasn't. "Of all the days..."

Twilight burst into laughter. After a few more minutes, Ponyville was in sight. It was pretty foggy, much like the scene of a zombie movie. Or a novel. Twilight had read about the suspected 'End of Days', when the Elements of Harmony would turn against the realm they were created to protect. The power of the unleashed Elements would then erase life in Equestria. It was a rumor started so long ago. Much like the tale of Nightmare Moon, the story was forgotten.

She caught sight of her library. It looked the same as before. She looked around. Ponies were beginning their usual routines of opening shops and selling produce. She didn't see Applejack's cart though. "I don't see Applejack," Spike said.

Twilight nodded. Ever since she moved back to Canterlot, her friends kind of drifted apart. Applejack left to travel to Appleloosa for business. To her, it was an excuse to get away from Ponyville. Twilight would sometimes get a letter from Applejack, but it was only a status report.

Twilight found a nice spot to land without being seen. She would always be crowded by ponies in Canterlot, but that was for advice. She was the princess who didn't spend time in the throne room. She had no idea what she was in for the moment she landed in Ponyville. Her hooves touched the earth, and she sighed. It was good to be back.

Spike jumped off her back, and that's when it all happened. Spike burped, sending green flames into the sky. The scroll had appeared. Twilight levitated it towards her, but before she could read it, she heard commotion from behind the bushes. From behind the bushes, a crowd of ponies ran toward her.

"Spike, RUN!"

Spike jumped on Twilight's back, and she ran. Stallions had roses in their mouths. This motivated Twilight to run even faster. She saw the library in front of her. If she could get in, then she would be safe. She was about to perform an Unlocking Spell on the door, but it swung open. Inside was Pinkie Pie. "Twilight! Hurry up!"

She looked back at the crowd. They were getting closer. She poured her magic into her Teleportation Spell, and teleported to the doormat of her old home. She ran in, and shut the door behind her. Pinkie smiled as she turned the lights on. "TWILIGHT! GOOD TO SEE YOU AGAIN!"

Twilight collapsed. "Pinkie?! What the hay is going-?"

Pinkie shoved her hoof into Twilight's mouth. "They could be listening. Shhhhh."

Twilight rolled her eyes and used her magic to expunge the hoof from her mouth. "You were yelling a moment ago. What's going on?"

Pinkie smiled. "Well, nopony is still used to being in the same town as a princess. Ever since your coronation, everypony just wants to remember that they played host to a princess."

"Then explain the roses?!"

Pinkie laughed. "Some want to remember more."

Twilight groaned. First was the whole controversy surrounding her and the new guard of the Crystal Empire, now it's this. This just proves that labels really do change things for you. "I guess you finally had time to yourself today, huh?" Pinkie asked.

Twilight nodded. "Princess Celestia sent me a letter saying there was trouble in Manehattan and she was tending to the matter. Strange thing is, all the guards were at their posts as I was leaving Canterlot," she said.

"Maybe they are the fallback. You never know, something could happen."

"Good point Pinkie."

Twilight looked around at her library. Except for the fact that all the books were dusty, everything was the same. The scorch mark on the floor when she was teleported, the stallion bust in the middle of the room, and the glass case that held the Elements of Harmony was undisturbed. Spike left to check the kitchen while Twilight picked a book from the shelves and began to read.

Pinkie paced around the library. She occasionally picked a book, flipped through the book, and dropped it on the floor. This alarmed Twilight. Pinkie was never this nosy. She never threw books on the ground without care. Pinkie stopped at a few books and put them on the center table, but that was all she did. "Hey Twilight, I've been wondering."

"About?"

She pointed at the glass case. "Can anypony lift that case?"

Twilight raised an eyebrow. What a weird question. "Just me. I enchanted the glass so only I can lift it. It now works on alicorns just in case Princess Celestia needs them for something. Why do you ask?"

She shrugged. "I was just wondering. I spotted someponies wandering too close to the library several times while you were away. I was wondering if stealing the Elements was even possible."

A burp erupted from the kitchen. Twilight rolled her eyes. "Spike, you know some of that food is old, right?"

"Twilight, I'm not eating. It's another letter from the princess," Spike called out.

Twilight stood and walked over to the kitchen. Spike held up the letter, which had a black ribbon tied around it. Twilight had never seen a black ribbon letter before. She unraveled it and began to read. Immediately she felt chills running down her spine.

_Twilight!_

_Listen to me very carefully. Disregard the letter from me earlier. I never sent you a letter about Manehattan. You need to secure the Elements immediately! You are in terrible danger. Do not react to this letter in any way around anypony. Nopony must know that something has happened. I've alerted the guards. Be ready to evacuate Ponyville. Oh dear Me, they found me. Be careful Twili_

The letter stopped there. It was in Celestia's writing, she was sure of that. It appeared to have been rushed. Her name was dragged out in black ink. On the top corner, a large blot of ink stained the paper.

Suddenly, she heard a sigh from behind her. Twilight and Spike turned to see Pinkie behind them. "And we were so close." Her eyes glowed green.

Twilight gasped and took a fighting stance. She shielded Spike. "Spike, get out of here!"

Spike turned to run, but was suddenly hit with a green light. Twilight turned to see Spike sprawled across the floor. He was knocked out. Above him was two changelings with their magic auras charged up.

Twilight summoned a Stunning Spell from her arsenal of combat spells. Before she could fire, she was hit upside the head by something hard and metal. Her last moment of consciousness was three changelings standing proud above her. Behind them, Queen Chrysalis was grinning. "Looks like you left your guard down, Princess Twilight. How very unlike you."

Twilight tried to force a sentence to rebuttal, but fell prey to the pain and passed out.

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><p><strong>AN: Chapter 2 complete. Please review your thoughts on this chapter, and I will return with a new installment. Anything helps.**

**-SirScribe**


	3. Train ride gone south

**A/N: The Sochi Olympics. Quite a bit going on with that I bet. I'm not watching it, but it does set a good example. The whole world comes together for a few weeks without any fighting. I only hope that, in the future, this unity will last forever. Anyway, welcome back to Dark Vengeance! I've been working on this project for a long time, and it is really fun. I've had the chance to experiment with a completely different way of writing. If you haven't heard, I'm also Newage416 on the Percy Jackson Fanfics. Going from Rick Riordan to Lauren Faust is really a transition. I hope to please the bronies and pegasisters on this site much like the demigods on the other.**

**Pinkie: Demigods! WHOOOO!**

**Me: Seriously?!**

**Pinkie: Demigods are new! Besides, have you met any demigods?**

**Me: I've been chased by several owls thanks to Athena and her children.**

**Pinkie: Cool!**

**Me: No, not cool! Do you know how hard it is to clean up after being chased for 5 hours by owls and kids with swords?**

**Twilight: Owls aren't too bad.**

**Me: You should've been there Twi. Anyway, let's get started. I don't own MLP. All rights go to Lauren Faust and Hasbro.**

**Pinkie: OWL!**

**Me: *runs under table* WHERE?**

**Pinkie: *laughs***

**Twilight: *chuckles***

**Me: You two are mean. Anyway, ONWARDS!**

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><p>Applejack was on the train when the attack occurred.<p>

Ever since they got back from the Crystal Empire, Princess Celestia requested that Twilight move permanently to Canterlot for her studies on becoming a princess. Even though she learned a lot, Twilight still had a lot to learn. Celestia's request ripped apart the Mane 6. Rainbow and Fluttershy returned to Cloudsdale, Rarity continued living in Ponyville along with Pinkie. Applejack, well, decided to travel.

Applejack traveled throughout Equestria in search for something to occupy her life since Twilight left. She spent most of her time in Appleloosa to oversee the Apple business. Still, it was an excuse to get out of Ponyville.

Applejack was at the station when she heard what was going on. Rumors began to circulate that Princess Twilight was in Ponyville. Applejack lit up. It had been a while since she had seen her friend, and since she was in Ponyville, it was a great time to catch up. She changed her ticket for one to Ponyville, and boarded the train. She was full of happiness. The gang was coming back together.

Figures that when you want to get somewhere in a hurry, something has to happen to stop it. The train broke down half way through Ghastly Gorge. Applejack groaned. Train delays were always something to get frustrated over. She looked around the train. Other ponies were confused and angry over the train delay.

Applejack was about to go to sleep when she heard something familiar. "You must let Trixie leave the train! Trixie demands it!"

"Sorry Trixie, but you can't! We are currently stuck in the middle of the Gorge. You must wait until we get to Ponyville before you can change trains," the conductor said.

Applejack spun around. Sure enough, Trixie was in the back arguing with the conductor. Applejack rolled her eyes. Figures that Trixie would cause a commotion. Trixie spun around and immediately saw Applejack. Trixie walked past the conductor and sat next to Applejack. "What do ya want?" Applejack asked.

Trixie's ears fell. "Look, can we look past what Trixie did in Ponyville?"

Applejack looked over at her. "No!"

Trixie sighed. "Listen to Trixie. You can't go to Ponyville."

Applejack laughed. "And why shant I go back? Ya hiding somethin'?"

Trixie said nothing. "Just don't get off the train in Ponyville. You were safe in Appleloosa," she said.

"Ya threatenin' me?!"

Trixie violently shook her head. "Listen to Trixie. Don't go back to Ponyville. It's dangerous!"

Applejack ignored her. The train jerked forward and continued moving. Ponies on the train began to cheer as the train sped up. Trixie's reaction was just the opposite. She got off her seat and walked toward the back of the train. This fueled Applejack's curiosity. Why would Trixie go through all that trouble to tell her not to go to Ponyville? She looked back to see Trixie entering the car behind hers. Applejack sighed and followed the showpony to the back.

When Applejack walked in, she saw several suitcases. She had her hat and cloak on a hat rack, which she began to don. She looked like herself physically, yet she didn't look the same emotionally. Applejack walked over to the magician. Trixie noticed and immediately took a few steps back.

"Ah don't want any trouble, just to talk," Applejack said.

Trixie didn't lower her guard. "Why'd you say to not go to Ponyville?" she asked.

Trixie rubbed her hoof nervously. "You all made enemies, right?"

Applejack nodded. "Well, Trixie got a letter a few weeks ago. It's something you would not like."

Using her magic, Trixie levitated a scroll from her cloak and opened it in Applejack's face. Immediately, something wasn't right.

_Trixie Lulamoon,_

_I understand that you have an neverending grudge against one Twilight Sparkle and her friends. You are not the only one. I have created a team designed to get revenge against Twilight, the Princesses, and pretty much all of Equestria. I know you want to be remembered as the unicorn to beat Twilight, and I can make your dream a reality. You can truly be the Great and Powerful Trixie._

_Write back your response. I expect a lot from the Great and Powerful Trixie._

_-Discord_

Applejack's jaw was touching the floor. "Discord? But he's reformed!"

Trixie retracted the scroll. "Trixie wants to be Twilight Sparkle in magic, no doubt about it, but Trixie doesn't want to hurt her. Trixie turned down Discord's proposal and wanted to warn the princesses, but Trixie couldn't. When Trixie heard of Twilight appearing in Ponyville this morning, Trixie knew that today is the day. Day X," she said.

Applejack was at a loss of words. Day X? She looked up at Trixie. "If what ya sayin' is true, then Twilight..."

Trixie nodded. Suddenly, the train jerked to the side, knocking Applejack and Trixie into the wall. The impact almost knocked out Applejack, luckily Trixie stopped her fall using her magic. Applejack looked up at the unicorn and nodded. "Mighty thanks," she said.

Trixie nodded in response. The two mares got up and looked around, looking for any sign of damage. Trixie's ears started twitching. Applejack could also hear something. Something was going on on the other side of the doors. Applejack opened the doors, and gasped. The whole car was filled with changelings attacking innocent mares, stallions, and fillies.

Applejack looked over at Trixie. Her face said it all. _It's starting._

She turned to the magician. "Listen Trixie, ah know we had our differences, but ah need yer help. Help me stop these here changelings!" she said.

Trixie backed away. It was like the Ursa Minor incident all over. She talked the talk, but she couldn't walk the walk. "Listen Trixie, innocent lives are in danger. Ya gotta help me get rid of em. Please Trixie!"

Trixie sighed and fixed her hat. "Let's go."

Applejack smiled. They both turned their attention to the swarm of changelings. With a loud cheer, the mares charged into the swarm. Applejack went for a serious buck in the face of one changeling. The force of the kick sent it into a small group of 10 changelings. They fell like bowling pins. She went around, kicking every single changeling that ever came close to her. Some flew out the window by the power of her kick.

Trixie was having a cleaner fight. Using her magic, she fired several Stun Spells at the changelings, knocking them out. Some changelings took notice and began to charge the magician. She had no choice but to duck and dodge every single one of their charged. She continued to fire spells at the changelings. Some got the idea to use shields against the magician, but she was already one step ahead of them.

Thanks to an idea she got while traveling, she was able to use some gunpowder from her magical arsenal. She had wrapped them up into some cloth, and with a simple flame, she had portable fireworks. She just to happened to have some in her cloak. She removed some, and threw them at the changelings. Firing an Incendiary Spell, the bombs caught fire and blinded many changelings.

Applejack was impressed. She reached under her seat and pulled out her rope. She lassoed a changeling, and used it as a hammer against the others. The changelings were smart to duck, well some of them. Some changelings were shot straight out the windows (whatever was left) and into the bog they were passing. She let go of her hammer and lassoed something else: somepony's suitcase.

"Hey, I need th-"

Applejack ignored the stallion as she swung the case. It nailed a changeling in the eye, sending it to the ground. This was a better hammer. She swung and hit as many changelings as she could.

Trixie's magic had greatly improved since her last visit. Using some Transfiguration Spells, she turned changelings into pots of flowers. She was about to nail a changeling with a spell to turn it into a toadstool, but a blast of green energy hit her hat. It was knocked off her head. She turned to grab it, only to see a burn mark in it. The green energy burned right through. Immediately she began to tear up. Her sadness quickly evolved into something else.

Trixie's anger flared. Her magic aura turned red. She started firing magic spells left and right at the changelings. Applejack thought that the fight would soon be over, but the changelings kept coming. She was running out of breath. She couldn't fight forever.

She was knocked toward the window by a changeling. As she wrestled with the changeling, she managed to take a peek at the sky. She noticed something in the distance. Something moving fast and her way. Instantly, she knew who it was. She looked over at Trixie, who was still firing spells. "Trixie, ah advise ya get down!"

Trixie looked over. She noticed the small streak in the sky behind her. Whatever it was, it was coming in fact. She nodded. She looked back outside. It was getting close. "EVERYPONY GET DOWN!"

All the ponies dove to the floor. Not a moment too soon. Right as Applejack dove for the floor, a large explosion rocked the train. Following the explosion was a bright array of lights. Trixie looked outside to see the lights. Her eyes lit up with the colors. She had never seen anything so beautiful in all her life. No amount of magic could ever mimic it.

The changelings immediately fled the train. Some were immediately met with a pegasi offensive. Applejack had to only laugh. "Ya better run! Ya think one unicorn and earth pony was bad?"

Trixie had to laugh as the changelings fled. When she looked back at her hat, though, her joy was replaced with sadness. _My last memory, burned._

Applejack looked over and noticed Trixie's sadness. She went over to the unicorn to comfort her. That would've happened if somepony didn't interrupt. "Did you see that?! One Sonic Rainboom scared those changelings! Another awesome feat by Rainbow Dash!" RD said as she flew into the train.

She stopped when she noticed Applejack and Trixie. Trixie was holding back tears while Applejack was comforting her. "Applejack? Trixie? What are you two doing here?"

Applejack looked up. "Ah was going to Ponyville to see Twilight before all this happened. Trixie found me," she said.

Rainbow looked over at Trixie. "Trixie, did you have something to do with this? Huh? Did you lead the changelings here?"

"RAINBOW!" Applejack yelled.

Rainbow only shrugged. Behind Rainbow Dash flew in Fluttershy. She looked mighty tired from trying to catch up to Rainbow. "Oh, am I interrupting something?"

Applejack didn't have a correct answer. "Look, Trixie is having a problem. Rainbow, ah want you to lead the train to Ponyville. We gotta get these here ponies to safety. Fluttershy, can ya check on the passengers?"

Rainbow Dash saluted and flew back outside. Fluttershy flew in, and started helping ponies up. "Um, Applejack, there's something I need to tell you," Fluttershy said.

Applejack looked up. "Um, I was in Ponyville earlier, and I saw Twilight. She was in her library, and I was about to visit, but something happened."

"What do ya mean?"

Fluttershy took a few steps back. "I, um, I heard Twilight scream."

Trixie looked up. "Sweet Celestia, they got her!"

Applejack and Fluttershy gasped. "You know?"

Trixie nodded and gave Fluttershy the scroll. After a while, Fluttershy began to tear up. That lasted for only a moment. Her sadness was replaced with anger. "How are Discord do this! HE'S OUR FRIEND! AT LEAST THAT WAS WHAT I THOUGHT HE WAS!"

Trixie nodded. "We gotta get to Canterlot Castle. Ah have a feelin' that's where Twilight is," Applejack said.

Trixie nodded once again. Rainbow appeared at the window. "So we're going to Canterlot?"

Applejack nodded. "Alright, ALL ABOARD FOR CANTERLOT!" Rainbow cheered.

Rainbow flew to the back of the train. Using her strength and speed, she blasted the train through the town and toward the royal city.

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><p><strong>AN: Another chapter done. I had to do at least a little bit of Trixie in this one. I don't know whether or not to have her fully included in the story, or have her in the background throughtout the story. Leave your suggestions in the reviews. The original copy of this was a lot longer, so I decided to cut it in half for your sakes. Anyway, I hope you enjoyed, and have a great morning/afternoon/night. Peace out!**

**-Sir Scribe**


	4. Canterlot

**A/N: Greetings everyone, SirScribe here with another installment of Dark Vengeance.**

**I have published a poll on my profile that relates to this story. Actually, I'm thinking on expanding. Please vote on the poll, it will help me in the future. Now, let's get this *looks around* party started.**

**Pinkie: I heard somepony say party.**

**Me: It was the neighbors**

**Pinkie: They're having a party? Sorry Scribe, but I have to go!**

**Pinkie *zooms away***

**Me: Did that actually work? Hmm, should've done that a long time ago. Anyway, let's get started.**

**Disclaimer: The only things I own in MLP are Silverstar the Wicked and Scribe.**

**Me: Silverstar the Wicked is a new OC I've developed. Yes he is an alicorn, but he is not going to be OP or the next ruler of Equestria. It's, uh, it's a bit difficult to explain without giving too much information. Anyway, ONWARDS AND UPWARDS!**

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><p>Thanks to Rainbow Dash's quick thinking, she moved everypony to the back of the train while her friends moved to the engine. When the train came into Ponyville, Rainbow Dash had the ponies exit the train. Detaching the engine from the rest of the train, Rainbow pushed the train engine forward. Fluttershy grabbed a hold of the controls, and like a professional, ignited the fires of the train. Rainbow had to try to keep up with the train thanks to Fluttershy. It got them to go faster, and that was good enough for her.<p>

What really made the trip enjoyable was Applejack's thoughts racing. Of course, she was worried about the rest of her friends, but one pony in particular crossed her mind. Somepony who deserved a second chance. Trixie.

Trixie elected to get off with the other ponies at Ponyville. It took a while and a lot of arguing, but they finally agreed. Ponyville needed magic to defend its borders from invasion.

"Ya sure about this?" Applejack asked her.

Trixie nodded. "Trixie-er I mean I- believe that my business is better here. Besides, I need to fix some broken roads."

Rainbow gagged in the background. Fluttershy gave Rainbow a look that was too perfect. "We need ya help Trixie, but if ya really think this is best-"

Trixie smiled. They touched hooves and went their separate ways. Applejack boarded the train, but before she closed the door, she turned around to face Trixie once again. Trixie was standing next to a trash can. Her hat glowed in her pink magic aura, and it levitated into the empty bin. Applejack's heart broke. Maybe something could be done. Applejack smiled. She knew what to do. She closed the door behind her, and the train took off.

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><p>When the train pulled into the station inside Canterlot, the three friends found themselves in the middle of a war zone. Entire shops were blown up from within. Mannequins with stylish gowns and tuxedos were thrown all over the city streets. Glass littered the sidewalks. Guards in full armor littered the ground. Some were alive, some weren't. Fluttershy walked over to one to check for a heartbeat.<p>

She got something different.

As she got close, she noticed something different about the pony. There were no injuries on him. No blood, no blunt injuries, no nothing. The pony seemed to only be passed out. Fluttershy placed her hoof on the pony's head, and that's when it happened. A green glow enveloped the unconscious pony. Fluttershy squeaked and flew back to her friends. Rainbow Dash rolled her eyes.

"Changelings? But how-?"

"I guess we were the distraction," Rainbow said.

Fluttershy hid behind Rainbow. "W-why are th-they here?"

Applejack lowered her stetson. "Ah don't know, but ah would like to find out."

Rainbow smiled. "Let's go ladies! Canterlot is not saving itself!"

"Wouldn't that be amazing," Applejack muttered.

Rainbow was about to fly towards the castle, but suddenly stopped. In front of her was a cage made entirely out of...smoke? The bars were shifting within the darkness, like it was deciding whether or not to be cell bars. The cage had two ponies inside. One was the pompous Prince Blueblood. The other was...Rarity? The fashionista was knocked out on the floor of the cage next to Blueblood. It took all of Rainbow's willpower not to laugh at the sight before her. Rarity would go on rants concerning that night at the Gala when she was treated like garbage by the prince.

Fluttershy flew up and nearly shrieked. "Rarity?"

The unicorn stirred in her sleep. "Not now Sweetie Belle, go play with your friends," she muttered.

Applejack raised an eyebrow. "Ok, A'hm done here. HEY RARITY, WAKE UP!"

Nothing. Rainbow tried rattling the cage, but it didn't move. It felt heavy. "Rarity, please wake up, if you want to," Fluttershy said.

Rainbow rolled her eyes. "The boutique burned down," she whispered into the cage.

In a flash, Rarity was at the cage looking like a maniac. "WHO DID IT? IS SWEETIE BELLE SAFE? WHAT HAPPENED TO MY SUMMER COLLECTION?! I'LL HAVE THAT PONY'S HE-"

Rainbow Dash started laughing uncontrollably. Fluttershy managed a weak smile while Applejack just shook her head. "Nice to see somepony still has her priorities straight," she said.

Rarity looked down at the farm pony. "Excuse me for thinking about my work."

Applejack smirked. "Rarity, what are ya doing up there? Cages aren't your specialty," she said.

Rarity sighed. She looked around, and immediately went into panic mode. "This-this monstrosity! The ugly shades of black and purple just do not make a cage pretty. This horrid craftsmanship is enough of a punishment. Get me out of here!"

Fluttershy flew to the cage door located on the other side. She tried opening it, but found it locked. Rarity sighed. "Well, it could be worse. I could be stuck in the same cage as- OH NONONONONONONONONO!"

She kicked Blueblood's hoof away from hers. Even when unconscious, he still had to be laid down properly. "I don't care how you get me down, JUST DO IT QUICKLY!"

Applejack smirked. She threw her hat down and revealed her lasso. She threw the hoop at the lock on the cage. Then, she started rocking the cage back and forth, but very slowly. The cage was heavy enough for it to be almost impossible. Luckily, Twilight's rambling was still fresh in her mind.

_With enough momentum, any object can move. Just as long as somepony is able rock said object back and forth, it will be easy,_ she said.

Applejack could feel the rope started to give away, but she needed it to hang on for just a little longer. The cage was now violently rocking back and forth, throwing Rarity all over the cage. Her mane was all over the place, but not Blueblood's. Figures.

Suddenly, the cage flew off the hook it was hanging on. Rarity grabbed onto the nearest bar, and braced herself. The cage hit the ground, and cracked the pavement below. The cage door slowly opened, but Rarity flew out faster than Rainbow Dash could make a Rainboom. Speaking of Rainbow, the cyan pegasus was still laughing her mane off at the sight before her.

Rarity growled like a lion, but sighed. "Thank you Applejack. Although, when I say 'I don't care how you get me down', you should consider that I mean 'Get me down from here posthaste without damaging my mane'."

Applejack rolled her eyes. "Nice to see ya too Miss Prissy."

Rarity smirked and hugged the earth pony. "Applejack, where ever did you go? You disappeared from Ponyville, and everypony was worried."

"Ah needed to travel. Ah was just bored with tha scenery," she said.

Rainbow nodded. "Feels good huh?"

"Mighty so. But, ah missed the family. Ah heard Twilight was in town so ah hopped on a train to get here."

Rarity perked up. "Twilight? Twilight was in Ponyville?"

Fluttershy nodded. "This morning I was going to pick some flowers for Angel, and I saw Twilight run toward the Library. She seemed busy, so I didn't go talk to her," she said.

Rarity smiled. "And dear, I do apologize for missing our spa days. I promise to make it up to you in the future."

Fluttershy smiled. "You don't have to do that-"

"Oh, but I insist. And to make it up to you, once this is all over, I will treat everypony to a grand day at the spa here in Canterlot. You thought the Ponyville spa is amazing? Wait until you try-"

"Ah, girls, ah think that's enough," Applejack said.

Rarity chuckled. Rainbow went to check on the knocked out Blueblood. He didn't move nor speak. He was out cold. "I don't think Blueblood is waking up sometime soon," she said.

The girls all agreed and proceeded to move. All of a sudden, thunder clouds rolled into the city. The wind started to howl in the day. A crash of thunder scared Fluttershy to the point of unconsciousness. Luckily, Rarity was there to help calm her down. They all were.

Rainbow landed on a pile of rubble to avoid the winds. They were picking up quickly, and these clouds were moving on their own. A crash of thunder followed a blast of lightning. The bolt pierced the clouds, and a chariot was seen flying towards the city of Canterlot. The ponies all backed away as the chariot got closer. Behind the reins was a pony in a black cloak.

Fluttershy backed a bit farther than the rest. She suddenly stopped when she realized something was behind her. She turned around, and there was her now ex-best friend: Discord. He gave her a small wave. "Why hello Fluttershy, it's been a while."

Fluttershy stood in shock and anger. "Discord? So it is true! You decided that, even after we forgave you for everything you did, it was a good idea to do this? To turn against your friends?"

"Where's the fun in being good? It's so much better being bad," he said, donning a curly mustache seen on the faces of movie villains.

The blood began to boil. She was about to launch herself at Discord, but he disappeared in a flash bang. Fluttershy landed face first into a patch of grass. The group turned to see Fluttershy eating grass. They heard an echoing laughter from their favorite draconiquus as the scene in front of them turned into smoke.

"Discord! Ya two-faced traitor!" Applejack yelled.

"Bring it on, Discord! I've always wanted to do this!" Rainbow shouted.

The smoke died down. In front of them was the cloaked pony. They all knew who it was. The hood came down, and the face of Nightmare Moon was burned into the minds of all the ponies. "Well, look what we have here. The 4 ponies who stripped me of my power. That failure will be made up here, tonight."

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><p><strong>Cliffhanger! HA! I hope you like this chapter, because the next one will be ready soon. I recently started school once again (in fact, my first two classes just ended a few hours ago.) Hope you all have a great dayafternoon/night. I'm hoping I at least get these stories done before I go on a hiatus. So much to do as a college student. I'm sure some of you understand. Anyway, until next time!**

**-Scribe**


	5. Discord and Nightmare Moon

**A/N: Greetings everypony! First, I must say, thank you for the support! The reviews don't say it though. It's the views. I checked today how many views and visitors, and it is just amazing. I promise that this will be the jewel to this account. Although, I think that may change. Anyway, for a bit of news. First: I'm considering making an alicorn OC, HOWEVER, it will have flaws and will not be shipped with any of the Mane 6. It will not be OP. It will be a flawed alicorn who was slain during the beginning of the Early Days of Equestria. Remember, I'm considering.**

**Second: Season 4 is starting to slow down. It won't be long until that pesky chest is open and we see what is inside it. I am really hoping for a big finale. In ****_Castle Mane-ia, _****there was that bit with the Shadow Pony at the very end. If you didn't see that episode, surprise! Anyway, I'm hoping for the return of that thing.**

**One more thing: I hope you all have been checking out the poll on my profile. Every bit helps. Wow, it's been almost a month since I first started this account. So far so good.**

**Pinkie: THERE WAS NO PARTY NEXT DOOR!**

**Me: Oh dear**

**Pinkie: *Mane goes flat***

**Me: SOMEPONY HELP ME!**

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><p>The four friends stood back as Nightmare Moon appeared. Fluttershy was the most worried. Behind them, Discord was there tossing up an emerald like a bouncy ball. That's because whenever it hit the ground, instead of shattering, it bounced back into his paw. "I thought you all liked surprises," Discord said. "Looks like I was wrong."<p>

Rainbow flew up into Discord's face. "Listen here, buddy! You are going to reverse all of this right now before somepony gets hurt! I thought you were reformed!"

Discord rolled his eyes. "There's reformed, then there's patient. I never liked the princesses, and showing them that I had 'changed' made it easy for me to create the perfect storm!"

Fluttershy flew up to Discord. "You lied to us! You never cared about being our friend! You are just one great big MEANIE!"

Tears formed in Discord's eyes. "Fluttershy, I am so sorry. I promise you will never see this side of me ever again. Please, can you forgive me?"

As if on cue, Nightmare fired a beam of magic at Fluttershy. She shrieked as she fell to the ground. Rainbow rushed down to help her friend. "Fluttershy!"

The others rushed to Fluttershy's aid. Rainbow helped her friend to her hooves. "Um, thank you, um..."

Rainbow was confused. "Um, Fluttershy, are you OK?"

The pegasus nodded. "I don't know why my eyes are still clos- oh no."

Rarity moved closer to Fluttershy. "Um, darling, who is in front of you right now?"

Instead of answering, Fluttershy cowered and dropped to the ground. "Why is everything so dark? Oh Celestia, I-it's so dark. Ple-please somepony turn on a light."

Rainbow looked at her friends. "Sweet Celestia, my eyes are open. I can't see! I'm blind!"

The group gasped. Rainbow turned to Nightmare Moon. "You give my friend's eyesight back, or I'll-"

Discord snapped his fingers. Instantly, an apple lodged itself into Applejack's mouth. With another snap of his fingers, two anchors wrapped in chains ensnared the pegasus, sending her straight into the ground. The fall forced her to take a bite from the apple. Applejack was the next to take action. She readied her rope, and attempted to lasso the draconiquus.

It didn't work.

The lasso immediately turned into a snake. The snake hissed at the Earth Pony, forcing her to drop it. Rarity was busy trying to free Rainbow from the anchors. The process would've been quicker if Rarity didn't use a Hoof Filer to cut the chains.

Discord sighed at the sight before him. "Maybe this is a bit too easy," he said.

Nightmare looked at him. "And yet you were defeated by these pests...twice! You think this too simple?"

"Well look at them. One is blind, the other is weighed down, one is defenseless, and then there's Rarity. Believe me when I say that Rarity doesn't have an offensive abilities except for magic. I've seen what she can do, but that only applies with fashion. Face it, Nightmare, this is too easy," Discord said.

Nightmare facehoofed. "Well maybe it is without the Elements of Harmony. I thought you said the Elements were in Ponyville!"

"I told you, and you looked everywhere except where they are. You were probably standing right on top of it and didn't notice!"

"What is thou saying about thee?! That I be a blind fool?"

Discord cracked a smile. "If that's what you want to call it, sure. You 'be a blind fool'."

"TIS A LIE DISCORD!"

"Says the pony who knew Celestia had control over the Elements of Harmony! You knew the Elements were her new weapons, and you didn't bother trying to eliminate them?"

Nightmare's horn lit up. "How about I correct a small flaw in this plan!"

Discord summoned two Chaos Cannons: devices that were able to spread chaos anywhere and everywhere without wasting energy. "Bring it on, Moon Butt!"

Nightmare fired a magical beam at the god of Chaos. He simply dodged it and fired one of his cannons at Nightmare. A direct hit on the snout gave Nightmare an uncontrollably growing mustache and beard. Another shot fired and gave Nightmare a DUNCE hat.

Nightmare formed a pair of scissors and snipped the beard and 'stache. She shook the cap off her head. She fired a magical blast at Discord's Chaos Cannon, turning it into a bunch of bats. Discord rolled up his imaginary sleeve. "Oh it's on!"

With a snap of his fingers, Nightmare's wings turned into Jell-O. A pink cloud of chocolate milk rained down on the Princess of the Night. Her facial expression said it all: you've got to be kidding me. Discord reached over and plucked Nightmare's horn from her head and used it to scoop up the cloud. At first, Nightmare had no idea how to react. She just punched Discord, forcing him to drop her horn.

Discord sat straight up and summoned a glass of chocolate milk. He threw it at Nightmare's head, luckily she managed to duck in time. The glass flew over her head and exploded behind her. Nightmare turned her head to the crater left behind. Inside was a couple of Jack-in-the-Boxes crawling out and breaking into shops nearby.

Nightmare charged her counterattack. She fired a beam, hitting Discord's cloven hoof. Immediately he was engulfed in a black smoke. He shrieked as the smoke encased him. Nightmare fashioned a victorious grin. "Would'st thou apologize for thy offensive comment about thee?"

Discord laughed from within. "No way, Jose!" he called out.

Nightmare's victorious grin changed to a confused look. "And who is this 'Jose'? Is he one worthy opponent?"

Instead of answering, a block of ooze flew out of the smoke, nailing Nightmare in the muzzle. The cloud disappeared, leaving one dazed draconiquus behind. He looked over at the alicorn. She was covered in the ooze that sailed through the sky. Discord walked over and leaned into her face. "Checkmate, Nightmare."

Nightmare sighed in defeat. "Perhaps thou art correct. Perhaps this affair in Canterlot is too mediocre. A complete victory is control over the Elements," she said.

Discord allowed the ooze to melt, allowing Nightmare to stand. "I suggest looking in Ponyville. I said that a billion times!"

"The Elements are not there. There is none there but workforce," she said.

Discord sighed. "Twilight hid them in her library! There are in a glass case, and-"

Nightmare raised her hoof. "Where are the ponies we had reigned victorious over?"

"They're right over he-"

He gestured to the spot where the 4 ponies were, but the only things that were in their places were a bunch of chains, a snake, and a knocked out Prince Blueblood. Discord's jaw dropped to the floor, clanking like a piece of metal. "That's not fair," Nightmare said.

Discord sighed. "And that's why ponies are the worst to lock up and forget."

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><p><strong>AN: I hope you enjoyed the little Discord V. Nightmare battle here. Sorry it was a bit suckish, but some feedback is welcome. Lately, I've considered moving my stories to (or is it .net?) instead of staying here. Let's see what the future holds. Anyway, until next time! **

-Sir_Scribe_


	6. Canterlot castle mayhem

**A/N: Greetings readers, and welcome back to _Dark Vengeance. _So sorry for not updating as often as I should, but eh, had some stuff I needed to do. Anyway, I hope everyone is having a good morning/afternoon/evening. Lately, there have been some road blocks. One of them was this. With a college schedule that eats up energy and a job hunt that I've delayed, I've come to the conclusion that I need to get stuff done here. With very little support for this and other stories, I wonder if I should cancel this project and all others. Hardly any support around here. I don't know. If I do leave this site, I will probably go to instead.  
><strong>

**I have one question for all of you. Lately, I've been hearing that Applejack is considered a background character and she hasn't been getting any love. I'm just wondering: what is your honest opinion of Applejack, if any? I would love to hear from you. Applejack, in my eyes, is very lovable, and I do have a fan crush on her. Why? Well, she isn't afraid of being herself. I know that's honesty, but still. Applejack has really caught my eye lately, and I feel she has gotten little to no love. That's why I'm hoping to change that. Anyway, onwards! (Sorry for the long introduction, just had to get some stuff off the top of my head)**

**Pinkie: Apple cider season is starting!**

**Rainbow Dash: YOU AIN'T GETTING 7 CUPS THIS TIME!**

**Pinkie: 6 cups?**

**Rainbow: 2 cups.**

**Pinkie: ...**

**Me: This better not turn into-**

***Pinkie's mane deflates***

**Me: You better get out of here Dashie**

**Disclaimer: I no own MLP. All rights go to HASBRO**

**ONWARDS!**

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><p>Rainbow hated being the rescued. She could've taken on Discord and Nightmare Moon without any struggle, even while weighed down. With Discord and Nightmare arguing on how easy their takeover was, Rarity unlocked the chains on Rainbow Dash's hooves, picked up Fluttershy, and took off. The girls followed suit.<p>

Applejack's mind was still racing. Discord, the draconiquus who they showed tolerance to, had betrayed them. It was expected, obviously, but for him to stand by and watch as Fluttershy loses her mind and nearly have a heart attack was too much. She felt like a disappointment. It was because of their combined power that Nightmare Moon fell, but now she was alive and ruler of the world. To know that their first night as friends proved nothing more than the fact that 6 different ponies can meet and call each other friends.

Rarity, being the unicorn who spent a lot of time roaming the castle, knew all the twists and turns they needed to take. She led them through hall after hall after hall. Along the way, they managed to run into some changelings. Applejack's hind leg strength proved to clean changelings easy.

Rainbow Dash sighed as they reached another endless hallway. "I could've taken those two without breaking a sweat," she said. "We should've stopped them while we had the chance!"

"Rainbow! Nightmare gone and blinded Fluttershy and weighed ya down on the ground. Mah rope turned into a snake and Rarity doesn't have combat spells, no offense," Applejack said.

Rarity shrugged. "I never did like the style of offensive magic. I mean, who would think using magic in such a cruel way would be acceptable?" she said.

Applejack shrugged. Fluttershy stayed silent. She was too afraid to speak in darkness, even if it is just her vision that is obscured. Rarity panted. "Anypony else want a turn?"

Applejack trotted over to Rarity and offered to take her for the time being. Without Fluttershy on her back, Rarity was able to stretch for the first time since the cage fell earlier. Applejack centered Fluttershy on her back, and they continued walking/flying. Occasionally, Rainbow would quickly spin around to see if anypony was following them.

Fluttershy once walked in on one of Twilight's many lectures to herself. She once heard that if one sense is obscured, the other 4 will become stronger. Without her vision, Fluttershy was able to tell how far the hall went. She heard the collective voices of Rarity, Rainbow, and Applejack. She was also able to pick up a faint whisper. Her ears twitched as she looked for the sound. The whisper was calling out to her. It was a collection of whispers all saying the same thing: _turn left._

Fluttershy didn't say a word, but then she heard something else. A voice she recognized all too well. "Left."

The trio stopped. "Um, what?" Rarity asked.

Fluttershy shrunk down. "Um, if it isn't too much trouble, I think we should turn left. That is-if you want to."

Rarity smiled and turned to the direction. Down the small corridor was a door. A single door, and it was ajar. Rainbow could swear she saw somepony move behind the door. Instead of silently checking it out, Rainbow burst toward the door. Rarity was too slow to use her magic to stop her.

Rainbow blew the doors wide open. The room inside was empty. A couple shelves of books lined the wall with several thrown about. A couch was turned upside down in the far right corner. In the middle of the room was a box. Rainbow immediately recognized it.

"Rarity, Applejack, come check this out!" she called out.

The two walked in. Fluttershy was busy humming to herself to calm her down. It seemed to be working since she had a grin on her face. "No way. Sugarcube, ya found the Elements!"

Sure enough, the chest containing the Elements of Harmony was sitting there on top of a pedestal. The box opened, revealing 4 necklaces. The girls gasped. Pinkie's Element was missing. Since Twilight used her Element as a crown, it was more than likely with her. Rarity levitated the Elements to the girls before she put hers on. Before she did, however, Pinkie happened.

There was a loud battle cry. Rarity just had to look up to see Pinkie falling from the ceiling. Rarity was too late to react, and was immediately squashed by the bouncing pink pony. Fluttershy did a quiet giggle before she felt somepony staring at her. Applejack flat out laughed at the scene before her. Ladies and gentlemen, the Element of Honesty.

Rainbow helped Pinkie from Rarity, who was about ready to get her hooves dirty for a bit of payback. "Pinkie, what in the name of sanity were you thinking?" Rainbow asked.

Pinkie shrugged. "Had to see if she is a changeling," she said.

Rarity sighed. "Darling, you didn't have to drop from the ceiling just to see if I was a changeling. I am not a changeling," she said.

"Prove it."

Applejack facehoofed. Rarity sat there pondering ways to prove to Pinkie that she was the real deal. "Um, when we were stranded in the desert, thanks to somepony, I was questioned on whether to call your new treat a Chimicherry or Cherrychanga. We spent a good few hours in the desert debating over the subject before we caught a train to Ponyville."

Pinkie leaned into Rarity's face. Rarity could feel the party pony staring into her soul. "Okey-dokie!" Then she hopped away.

Rainbow watched as Pinkie left. She was about to say something, but shook her head and flew out the door. Rarity looked up at the ceiling. "How did she ever get up there?"

"Beats me. Ah never question Pinkie anymore, not since the Mirror Pool thing," Applejack said.

"Or the pre-birthday party for Angel," Fluttershy said.

Applejack sighed. "Poor Angel. Is therapy doing OK?"

"Oh yes! Angel has made progress, but I cut out the cucumbers in his salads. We don't want to have him remember the party," Fluttershy said.

Rarity began to remember the party, and shook it out of her mind. Only Pinkie can find a way to shove 15 cucumbers in Angel's mouth with a candle at the end of each. She grabbed Pinkie's Element and chased after her. Applejack fixed Fluttershy on her back and began to walk out the door. Before she did, however, she noticed something on the corner of her eye. A creature was in the corner of the room. It was an adult-sized animal. The animal was sandy colored and seemed to be staring at the Earth Pony. Applejack ignored it and closed the doors behind her using her tail.

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><p>Pinkie was full of surprises as time progressed. Somehow, she had hidden a party cannon and pulled it out whenever a changeling looked their way. At the press of a button, the changelings would be covered in so much confetti, that it was impossible to get it out. Rarity was stunned at the Earth Pony's actions.<p>

The 5 finally came to the main hall. The doors in front of them were giant and without any guards. Applejack fixed her stetson. "Y'all ready?"

The 4 nodded. She took a deep breath and kicked open the doors. The scene inside was horrible. Queen Chrysalis and King Sombra were sitting at the throne of Celestia. Several changelings and shadow ponies surrounded the two monarchs. In the middle of the room was an injured Princess Celestia. Her horn was snapped in half. Above her was Twilight.

The recently crowned alicorn had an energy shield over herself and Celestia. Changelings were seen trying to find a way inside. The hammered at the shield with no success.

Sombra was laughing as the doors opened. He looked up and with a magic spell, cast a bright light over the 5. The girls screamed in terror as they felt pain erupt all over their bodies.

"Well, it looks like we have some visitors," Sombra said.

"Indeed. I do believe they should be comfortable if we want their company," Chrysalis said.

The last thing Applejack remembered was being covered in a green glow.

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><p><strong>AN: Well, there you go everyone. Because of school, this will be the last chapter for a while. Again, sorry for the hiatus. If you liked this chapter, please review it. It helps me a lot. Don't forget to Follow this story for more content. Peace out, and until next time**

**Keep Calm and Flutter On!**

**-SirScribe**


	7. Shadows have closed

**A/N: Greetings everypony! I hope you all are having a fantastic week. Sorry that I've taken so long to update. I hope I can make it up to you. This chapter has been one I've been looking forward to for a long time. Something about the video tiarawhy made revolving the alternate ending of 'Canterlot Wedding'. I've recently come into a new way of uploading since I was using the fanfiction site to write my stories. It started out as a great idea, and then there was the update. I am fortunate that I was able to upgrade. Maybe it will show in the new chapter.**

**Last chapter, Rainbow got into a bit of trouble with Pinkie Pie. For now, she is in Urgent Care and Pinkie has been restrained for the time being. It is not 'Cupcakes', but it was expected. Twi said that Rainbow will have a few drinks of apple cider once she is out of the hospital. The only problem is hiding all that drink. Oh well, let's get rocking. Also, with Pinkie and Rainbow out for the time being, my cohost today is Princess Luna**

**Luna: GREETINGS CITIZENS OF !**

**Me: Please no Canterlot voice**

**Luna: BUT WE ALWAYS ADDRESS OUR LOYAL CITIZENS WITH THE ROYAL CANTERLOT VOICE!**

**Me: They must've had horrible hearing after every royal proclaimation.**

**Luna: ARE YOU IMPLYING SOMETHING?!**

**Me: No! I-I mean, why not take it down a few hundred notches. 21****st**** Century is 'Royal Canterlot Voice' free.**

**Luna: But, we like the Royal Canterlot Voice**

**Me: I'm sorry, but times have changed.**

**Luna: …**

**Me: I don't think she will be coming back here any time soon. That is her decision. Anyway, let's get started.**

**Disclaimer: I don't own MLP: FiM**

**Luna: We shall begin!**

**ONWARDS AND UPWARDS!**

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><p>Twilight was happy to see her friends again. Ever since her visit to the human world, Princess Celestia and Luna sent Twilight all over Equestria to be better familiar with the realm. Her 3 days in the human world opened many doors for her and the royals. With new knowledge and possible goals put in place, Twilight needed to be sure everything for the future would be perfect. Unfortunately, she overlooked Discord's free time. Because of the limited restrictions on the draconiquus, Discord had managed to recover Sombra and Chrysalis. How Nightmare Moon survived was a mystery for all of them.<p>

When she had awoken from her sleep, Twilight immediately searched for Princess Celestia. After finding the Princess of the Day, the two decided to take on Chrysalis once more. With new spells in both of their arsenals, they thought they were finally going to win without the Elements. They thought wrong. With the appearance of Nightmare Moon, Celestia's guard was lowered. A magical burst of dark magic quickly incapacitated the princess. Twilight, however, studied various combat spells from Starswirl's journals. His extensive research on the matter proved to be helpful, yet she was limited. Much of the magic she learned either evolved into different forms of magic, or were labeled as duds. Because of that, she was put on the defensive.

Twilight held the shield up against the changelings. Nightmare, after realizing that she had no minions of her own, crafted Shadow Ponies to fight in her name. With Luna away on official business outside Equestria, no help was coming.

The doors burst open and her friends were easily overpowered. Her relieved emotions suddenly turned to dread. She nearly lowered her shield, but she stayed strong. Sombra looked over and chuckled. "I don't see the threat that Nightmare told us about," he said.

"It's hard to imagine that these 6 defeated us. At least Discord had the right idea," Chrysalis said. "So, what do we do with these 5?"

Sombra looked over at the 5 ponies sprawled out on the floor. "Well, the concept of 'Divide and Conquer' sounds like the best way to execute this."

Chrysalis smiled. She walked over to Applejack, who was chained by the hooves. Her horn glowed green and Applejack was bathed in the light. When it subsided, Applejack was on her hooves, bowing before Chrysalis. "Applejack!" Rarity shouted.

Sombra immediately spun around and eyed the unicorn. "Silence!"

She immediately did so. Chrysalis and Applejack returned to the throne. The earth pony had no emotion in her face, and that worried Twilight. "Now, are you going to surrender, or am I going to have to pick a henchpony myself?" Sombra asked.

Twilight looked over at her friends. They were all saying the same thing: don't do it. _If I surrender, maybe Applejack can be saved,_ Twilight thought.

The alicorn sighed and dropped the shield. The minute she did so, a Shadow Pony knocked her halfway across the room. She hit a column and slumped to the ground. Chrysalis laughed like a hyena. "Restrain her," she ordered.

A changeling and Shadow Pony flew over and pinned her to the column. Sombra sighed. "Finally, ultimate victory."

Rarity growled at her captors. "This is not how one treats a lady! I demand a better method of detainment!"

Sombra chuckled. He walked over to Rarity, and with the space between his horn and hers closing, Rarity felt fear engulf her. She shut her eyes, expecting the worst from him. In a flash of light, Rarity was let go. She wiped her eyes and turned to Rainbow Dash. Her eyes were green with a dark magic aura surrounding her horn. "RARITY!"

Sombra laughed. Rarity cracked a smile. "Oh wow, all this freedom! All this vast knowledge of the dark and artificial! This magic is more powerful than that of Celestia! I see why you used dark magic, Twilight. Dark magic is just so much easier to use than anything else. There are no rules for it! This is marvelous!"

Twilight looked up and felt dread. "But-but I surrendered! You leave my friends alone!"

Sombra looked over at the alicorn princess. "I never said I wasn't going to use them. I just got you to lower your shield. Remember child, you brought this upon yourself!" he said.

Rainbow grew angry and tried flying to rescue her friends, but suddenly, her wings felt heavy. Her wings fell to the ground along with her. She looked over, and realized that her wings became solid crystal. She tried getting to her hooves, but her wings were too heavy. She was trapped. Pinkie and Fluttershy were bound and tied by a changeling. "What possessed you to join forces?"

"Discord," Sombra said.

The draconiquus poofed into existence next to the king. "You called?"

"Without Discord's guidance and carefully thought out plan, we finally stood a chance against all of you. It is true that Nightmare Moon brought you all together, but it was Discord who discovered the weakness in the Elements: if one was inactive, then all of them are useless," Sombra said.

"By my power, I defeated Princess Celestia, but your brother got in the way. Lucky me that he has to protect his new home first. I've sent some of my children to the Crystal Empire to distract them," Chrysalis said.

"And by my power, I defeated the Empire. I've sent some Shadow Ponies, by the permission of Nightmare of course, and managed to corrupt the Crystal Heart. One puny distraction has turned into a perfect victory!"

Twilight tried moving, but her captors were too strong. "You know, I've read a lot of books about villains who talk about their plan and expect to get away with it, but it will never happen. Because you told me everything, I now know where to look and how to win," she said.

Sombra laughed. "If you can escape, then we've made a mistake. C'mon then, Twilight Sparkle, try to find help. You won't find any," he said.

Twilight smiled and shut her eyes. Her horn began to glow and her captors were turned into bunnies. Discord looked on with amusement. Twilight ran to the middle of the room and grabbed her Element of Magic. "My magic has doubled with the Element of Magic, Sombra! I can still beat you!"

She charged up her energy. Sombra sighed and played along. The two opened fire on each other. Their magical energy met in the middle of the room, bathing everypony in a bright light. Sombra was noticeably struggling under the Element's power. The beam inched closer to Sombra's horn. If their magic collided at his horn, he would be broken into pieces again.

Chrysalis tried stepping in, but was blocked by Sombra. "I can do this! I don't need help from an insect!"

"An insect?! How dare you!"

Chrysalis fired at Sombra, causing him to lose his concentration. Twilight was now an inch away from victory. Chrysalis noticed this, and added her magic into the mix. Twilight tried adjusting to the new source of magic.

She couldn't make it.

The power of combined magic against hers was too powerful. Her magic gave out, exposing her Element. The dark magic overwhelmed her, sending her out the window and into the dark abyss.

"TWILIGHT!"

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><p><strong>AN: Once again, I am so sorry that this took so long. With school clouding my mind, I just couldn't concentrate. I promise that I will get this done faster. I've put **_**New life in Ponyville **_**on hold since I somewhat lost interest in that. I may resume it as soon as I can, but for now, **_**Dark Vengeance **_**is on top of my priority list. Until next time, Flutter On!**

**-SirScribe**


	8. Welcome aboard

**A/N: Greetings everypony! Welcome back to **_**Dark Vengeance**_**! I feel like I'm on a roll: two updates in practically the same weekend. How is everypony these days? Um, I really don't know how to write the introduction, but I will answer a few reviews.**

**CoolCuttz: Thank you very much! I tip my hat back to you and you get a cookie (::)**

**Dark Sault: I wondered that too, and thanks to Tiarawhy, I can write how I think it will work**

**Just Call Me: Spike has been locked up by Chrysalis. He was taken while Twilight was knocked out. I may bring him back in later**

**Me: I was shocked with all of your reviews. I guess all of you want to see this thing go on. In that case, let the games begin.**

**MLP:FiM TV Time!**

**What did you all think of the newest episode of MLP that aired yesterday? Do not reveal any spoilers, but was it good to you? Was it awful? What do you think will be the next episode? Most importantly, what do you think is in the chest? Next to your review on this chapter, answer one of these questions, or all. Wow, I really don't know what else to say**

**Trixie: Speechless in the presence of the Great and Powerful Trixie? How expected**

**Me: Fillies and Gentlecolts, Trixie Lulamoon.**

**Trixie: Trixie was requested by SirScribe to attend today's recording. Of course, Trixie obliged to please her fans**

**Me: I thought you swore not to let your ego crash into the ceiling**

**Trixie: It hasn't!**

**Me: There's a hole in my roof**

**Trixie: Your home has poor construction work**

**Me: *facehoof* let's get this over with. I don't own MLP:FiM**

**Trixie: Let the show commence!**

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><p>Rainbow struggled to move. She just watched Twilight be blasted out the window with no remorse. Tears were forming in her eyes as she cursed at them for the first time in her life. Sombra smiled at Rainbow's anger and sadness and even produced a camera to record her cursing.<p>

Rarity and Applejack remained emotionless in the middle of the throne room. Chrysalis smiled. "As much as I wanted her gone, this was not what I expected at all," she said.

Sombra looked over. "If we decided to let her live, she would've found a way to overcome us. Her demise is necessary if we want Equestria all to us," Sombra said.

Chrysalis rolled her eyes. "Well then, with no more heroes of Equestria up your sleeve Celestia, it looks like this is victory," she said.

Princess Celestia raised her head. Her horn, still broken, started to run a familiar and red liquid. "You haven't won yet, Chrysalis. Remember, there are millions of ponies who will do whatever it takes to keep their families safe. You hit too close to home. Expect a revolution," she said.

Chrysalis smiled. "Guards, lock her up. Lock them all up. Send the yellow and pink ones to the dungeon! May they never see the light again," she said.

A few changelings walked over and carried the two ponies away, against their protests. Rainbow tried flying, but her crystalized wings were too heavy for any kind of movement. "Girls! Don't worry, I'll get us out of here! Fluttershy, don't be afraid!" she called out.

The door closed behind the prisoners. "And what of the rainbow one?" Sombra asked.

Chrysalis smiled. "Discord, have her sent to the Everfree Forest. Let her play with the monsters inside," she said.

Rainbow puffed up her chest. "I'm not afraid of the Everfree! I'm brave enough to take on anything in there," she said.

"When you can run. Goodbye Rainbow Dash."

Discord snapped his fingers, and Rainbow disappeared. Sombra laughed at her disappearance. "Now, Miss Rarity, I have an empire to return to, and I need somepony as my First General. Will you be willing to fight in the name of Your Highness?"

Rarity smiled. "But of course," she said.

Sombra smiled and teleported out of the throne room. Rarity followed suit. Chrysalis looked down at her slave. "Oh young Applejack. So very young and filled with sadness. You will be remembered beyond Twilight Sparkle. I have a pest problem at the apple orchards, and my changelings need help resolving the problem. How would you like to help your queen?"

"Ah would be delighted," she said.

"Good, now go. Your commanding officer will lead you to the first orchard."

Applejack turned and walked out the door. Chrysalis smiled. _Finally, victory!_

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><p><em>*Beep beep beep*<em>

The sound of a heart monitor slowly rocked Twilight back into consciousness. Her eyes slowly began to open, taking in her surroundings. She was in a hospital, a really weird hospital. She looked around. It was a single room and only one bed, and she was in it. The heart monitor was on her side, showing her that she is alive. She raised her head, only to be forced back down by pain. Her hoof instinctively ran up to her head. Bandages. She felt something warm underneath her bandages, and she guessed that it was blood. She groaned and slowly rose up.

Another painful shot ran up her head. This time, it was at her back. She looked over to see her wings bound to her body. She could only imagine her wings were broken. _3 months of having wings, and I break them. And how is Spike still well enough to be my assistant?_

Her eyes shot open. _Spike? Spike!_ She looked around, looking for her baby dragon. He wasn't there. Her heart monitor began to beep rapidly and she knew there would be a doctor coming in to check up on her. She needed to find Spike.

Immediately, the memories of what transpired in Canterlot flooded her mind. Rarity and Applejack becoming slaves of Sombra and Chrysalis, Fluttershy being blinded, Rainbow bound and helpless, and Princess Celestia near the point of death. She remembered trying to fight back with her Element of Magic, but it failed her.

She looked over at the counter next to her. Her Element was there, but the jewel was cracked. She read that cracking an Element was impossible, but it looks like it happened. _They won. I can't fight back, not without the Elements._

A hoof rested itself on her shoulder. She looked up. Princess Luna was there with a sympathetic look on her face. "Twilight Sparkle, it is good to see you alive," she said.

Twilight was at a loss of words. Instead of a simple 'Thank you', Twilight rose up and hugged the Princess of the Night. Luna was taken back at the sudden display of affection, but she hugged back. "Luna, I'm so sorry that I couldn't protect her. They have Princess Celestia. I'm sorry. I let you down."

Luna pulled the Princess of Magic back. "You did the best you could. You defended her while we couldn't. I am grateful that you were there for our sister."

Twilight nodded and pointed at the Element of Magic. "What do we do about the Elements? Mine is cracked."

Luna looked over at the crown. Her eyes were calculating several thousand thoughts in those 10 seconds. "We think we know somepony who can help you with this. He is here with his assistant. We are sure he knows what to do," he said.

Twilight looked up. "Is it Starswirl?" It was a farfetched question, but nopony else really understands the Elements as much as Starswirl. Luna shook her head.

"No, but he is close. He is as clever and wise as Starswirl. We will take you to him."

Twilight nodded. She jumped onto the floor, and immediately, the room began to shake. The shaking threw Luna and Twilight off balance. "I think that's him now," Luna said.

The Princess of Magic was confused. She followed Luna out of the hospital wing. In the hallway, there were engravings of strange symbols on the walls. They were not like the runes she studied from Pre-colonial times in Equestria. In fact, these runes looked older. Older and more powerful.

They reached the end of the hall. In front of them was a pair of gold doors. "We must warn thee, Twilight Sparkle, he is a bit eccentric. Patience is key with him," Luna said.

Twilight was confused. "Who is he? A magician? A scholar? A scientist? A doctor?"

Luna smiled. "All of them."

Luna opened the door. Twilight's eyes couldn't open any wider. She was in a very large room lined with copper. Frames extended from the floor all the way into the ceiling. In the middle of the room was a giant console with a large green tube running up to the ceiling. At the console was a brown Earth Pony with a messy mane. Next to the Earth Pony was a familiar gray Pegasus. She recognized the Pegasus from some of her endeavors. It was the mail mare who crashed into her balcony with a gift from Princess Celestia. Luckily she knew a spell to fix the vase.

The room continued to rock back and forth. The console began to explode, and the earth pony was trying to fix it. He flipped switches and pushed buttons at an unnatural speed. He was moving as fast as Rainbow. She looked up at Luna with a confused look.

Luna smiled. "Don't worry, he is a genius," she said.

Twilight looked back at the earth pony. He stopped and looked in their direction. He told the Pegasus something and walked over to them. "Luna, I can see you got bored with the library," he said.

"It's in the pool Doctor, we had to leave," she said, holding back a chuckle.

The words 'Library' and 'Pool' didn't seem compatible to Twilight. Why would the library be in the pool? The earth pony looked over at Twilight. Immediately, she recognized him. He would always be around whenever she or her friends got in trouble. It was him and the Pegasus who were there when she had to settle a dispute with the Appleloosans and buffalo tribes. He was there when Nightmare Moon returned. She ran past him when he was asking a question.

Twilight raised her hoof. "My name is Twilight Sparkle," she said.

He smiled. "Nice to finally be introduced to you, Twilight. I'm the Doctor."

"Doctor who?"

"Just 'The Doctor'," he said.

Twilight raised an eyebrow. Before she could question him, the room jerked forward. The Doctor turned to the Pegasus. "Ditzy, ease up on the controls! We aren't jumping into the Vortex this time!"

"I'm not trying to. They found us Doctor!" Ditzy called out.

The Doctor's eyes widened. "Alright then, it looks like we aren't staying here. Off we go!"

He ran back to the console. Twilight and Luna followed. The Doctor noticed them both. "Luna, I need you to keep that lever in the midway position! Twilight, press that blue button whenever it turns red. Ditzy, I need you on the shield. They are hitting us with everything they got!"

Luna and Ditzy ran to their stations while Twilight did nothing. The Doctor looked over to her. "Oh, and welcome to the TARDIS. _Allons-y!_"

The Doctor flipped a switch, and the TARDIS jerked forward. Twilight clung onto the console. She pressed the button as instructed. The Doctor and Ditzy were cheering. Luna was smiling while Twilight was starting to feel sick.

_I must be dreaming._

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><p><strong>AN: I hope you all like this little bit. I like the idea that someone combined Doctor Who with MLP. As he said, **_**Allons-y!**_

**-SirScribe**


	9. Mayhem in the control room

**A/N: Greetings people! I hope some of you enjoyed your Spring Break, unless it is happening right now. I don't get a Spring Break, so that sucks. Anyway, I looked at the reviews from the last chapter. I am so happy I surprised all of you. I've always wanted to do a Doctor Whooves moment, just I couldn't before. I was surprised to see Doctor Whooves as a character in the fandom. Why? Just because. Anyway, onwards. I am also planning on a Doctor Whooves spinoff from this fic. I already have a few stories planned out, it's the companion that I need to sort out. I know that Whooves' main companion is Derpy, but I wanna try something different. That's me after all. The Doctor Frankestallion! Well, I have the companion sorted out. Leave a guess as to who it is. This companion will be revealed towards the end of the story.**

**UPDATE: Starswirl's Nightmare and New Life in Ponyville are put on hold as of last week. I haven't really found any motivation, yet that doesn't mean that they will be deleted. I have to work some stuff out, and this week just hasn't been kind. I-I just feel different this week. I lost someone I cared about over the weekend and the news just hit me hard.**

**So season 4 is coming to an end sometime in the near future. I must ask: what was your favorite moment in season 4? If you haven't see the season or a specific episode, do not read the reviews. Let me know your favorite.**

**Rainbow Dash: One more step to the Wonderbolts!**

**Me: Ladies and gentlemen, Rainbow Dash**

**Rainbow Dash: Straight from Canterlot. Twilight sends her best and wishes everypony a grand day**

**Me: So Rainbow Dash, as well as other characters I've interacted with, know about the show. At first, they were creeped out, but then they looked over the fact that they were being stalked by humans. So long as they don't read 'Cupcakes' or find any, um, other art on the Internet, everything is fine.**

**Rainbow Dash: So I've heard season 4 of our show is coming to an end. Aw man, what Twilight does later on will be amazing! It will be so awesome!**

**Me: RAINBOW! Spoilers**

**Rainbow Dash: Oops. Anyway, let's continue. SirScribe doesn't own MLP. All rights go to Hasbro and The Hub Network.**

**Me: How long did it take to get over the fact that humans have watched your lives for years?**

**Rainbow Dash: Still trying to get over it. I have to watch what I do on my spare time nowadays**

**Me: Let's leave that to the imagination. Anyway, ONWARDS!**

* * *

><p>One of the many things running through Twilight's mind was, <em>Am I dead?<em> The answer was obvious. She was in a huge copper control room with a giant tower of nonsense with a stallion who has no name, a wall-eyed mail mare, and the Princess of the night. To her, those were the ingredients for a horrible story. A story that would follow her wherever she went in life.

The room rocked back and forth as the Doctor continued to speak gibberish. It seemed as though Luna and Derpy knew what he was talking about, which was impossible in her case. The Doctor threw a switch, and the entire room began making a noise. A loud screeching noise that raised the hairs on Twilight's coat. Luna reacted by throwing the same switch back in its original position. "We do not need to obliterate Twilight's hearing," she told the Doctor.

"Right, I'm going to have to fix that. I don't understand, I changed the Extrapolators a long time ago," he said.

"How long ago?"

The Doctor hit his head on the console. "Um, about a few minutes after you dropped Twilight off," he said.

Luna face-hoofed. Twilight looked down on the switches. The console was literally littered with bells, whistles, and sticks. Twilight pressed a button to only have the Doctor freak out. "Do you want to open a rift right above Canterlot?!"

Twilight looked up in shock. "A what?"

"A hole in the fabric of reality. A tear where time and space spill into the physical world. Do you want a tear in time and space to open up in a dense populated area?!"

Twilight's eyes widened. "No, not at all!"

The Doctor sighed and moved away from Twilight. The alicorn stood there as the Doctor continued to run around the console. Derpy looked over at Twilight, and pointed to the switch that was shaking. Twilight shrugged to herself and moved the lever. Immediately the room began to stabilize. Twilight could feel her heart beating louder than ever before. The Doctor looked over to where Derpy was, and chuckled. He continued flipping more switches before he stopped.

He was about to rest on a chair, but the room jerked forward again. "Shields are fading fast! I can't get us out of here! It's like there is a magical force field surrounding the planet, making it completely TARDIS proof," the Doctor said.

Twilight looked over. "TAR-what proof?"

"TARDIS. Stands for Time and Relative Dimension In Space. It's my time machine," the Doctor said.

Twilight looked at him for a moment. "You're joking. This cannot be a time machine. That technology is impossible."

"Yet there are Time Spells in the Royal Canterlot Archives in Starswirl's Wing," he rebutted.

"But that's just magic. You don't have any knowledge of magic. Unless you are hiding a horn under your mane, you cannot possibly travel through time!"

The Doctor smiled. "I would love to prove you wrong, but right now we need to get away from the Shadow Ponies chasing us. Derpy, what's the status on the shields?"

"They're going down fast. The glass thingy is saying 9 power," she said.

"9% power left? I thought I had more. Oh well, that's what happens when I have the shield on while playing Bowling for Asteroids. OK, it is obvious that the Shadow Ponies are stopping us from hitting space. What could it be?"

The mares stayed silent as the room shook. "C'mon, what's different in the world?!"

Luna was the first to speak. "Um, Nightmare Moon came back?"

"Nope! Derpy, what's new?"

"Chrysalis coming back?"

"Wrong. Twilight, what's new in the world?"

She shrugged. "You said Shadow Ponies."

"Exactly, Shadow Ponies. When Nightmare Moon first spawned into existence, she distributed so much dark magic into the castle that it latched onto any source of darkness. Her power gave life to the shadows, but that wasn't enough for them to grow, until…"

"The Summer Sun Celebration 3 years ago!" Luna shouted out.

"Oh yes! Nightmare Moon returns, and without Princess Celestia, the night time lasted a good 5 extra hours. Nightmare disbursed her magic all over Equestria, even latching a part of her life force onto a shadow for protection. She knew the Elements would be used once again and plotted against death."

"But that doesn't help us against the Shadow Ponies," Derpy said.

"Aha! But it does. Princess Luna returns with renewed ambitions to adapt and accept her role as Princess of the Night, leaving all that dark magic in the hooves of Nightmare. She rose an army against the Elements and soon had enough power to rise again," the Doctor said. "She grew a new army of living shadows to stop the Sun."

"They are keeping us from leaving Equestria. The Shadow Ponies must think we are a threat," Luna said.

The Doctor nodded. Meanwhile, Twilight was trying to build the picture. "Dark magic has encased the planet!"

"OH YES!" the Doctor said. "And getting past that much dark magic requires an equal amount of light magic. Luckily, we have two alicorns who are both gifted with extreme magical skills."

Luna and Twilight both exchanged glances. They silently realized what to do. Luna poured all her magic and energy into her horn, and so did Twilight. Immediately, their horns began emitting large amounts of magical energy. The console began to glow lavender and purple. The Doctor stood back along with his companion. Immediately, the TARDIS jerked forward, but not by the Shadow Ponies. The switches that the Doctor threw were going back to their original positions as the TARDIS accelerated.

Derpy began hovering in the air while the Doctor was taken for a roller coaster ride. The two alicorns continued focusing all their energy into flying the TARDIS, despite the rocking control room. Twilight knew that, in order to focus all magical energy into a complex task, she needed to think happy thoughts. Immediately, her mind reeled back to her first day with her friends. The day after the Nightmare Moon fiasco. Pinkie had staged a more 'formal' party welcoming her to Ponyville. She also remembered seeing Princess Celestia and Luna on her first week in Canterlot. She spent an afternoon with Princess Luna and tried teaching her the ways of the new age.

Her mind fast forwarded 2 years when she and her friends saved the Crystal Empire. The after party that Pinkie threw was enough to power the Crystal Heart for an eternity. The festivities were grand, but Twilight spending time with her brother and his wife was enough to make her happy. The week that followed Sombra's defeat was difficult for Princess Cadence since she used her magic to protect the Empire by herself.

_Twilight?_

A voice rang into her memories. She recognized the voice immediately. It was Spike. An image of the Canterlot Castle entered her mind. Nightmare Moon was sitting on Princess Celestia's throne with Spike standing by her side. He was dressed in an old jester's costume. In his hands was a chest with the 5 Elements of Harmony inside.

Twilight tried to turn away from the image, but then it flashed to Applejack knocking down her own apple trees. She and so many other hypnotized ponies were destroying Sweet Apple Acres. She turned her head away, but found herself in the Crystal Empire. Rarity was there in a military uniform, tearing down the defenses of the Empire. Princess Cadence and Shining Armor had their armies ready to defend, but they were quickly washed up by Sombra's dark magic.

"NO!"

One of the levers on the console ripped right out of the base, and the TARDIS began to spin. Alarms began to ring as everypony began screaming. All except the Doctor. He grabbed the broken lever and pulled out a silver device from the console. Twilight only got a glimpse of it. It was a silver stick with a blue light coming from the end of it. She saw him hit the underside of the lever with the light before he put it back into its empty slot. He shone the light over the spot before he threw it up. The lever was working again.

He galloped over to a large switch. "And we found it!"

The room stopped shaking. "Found what?" Twilight asked.

The Doctor pushed the final lever forward. "A weak point in Nightmare's line of defense. We are landing on the Moon very shortly."

Twilight's head began to hurt. "I think I'm gonna be—"

Twilight immediately ran into the hallway. The Doctor smiled and continued monitoring the TARDIS controls. "Just gotta park right here!"

He pulled back a switch and the TARDIS stopped. The engines died down as the Doctor grabbed the monitor. "We're here. The Lunar Ring of Maria," he said.

Princess Luna froze. "You brought us back to where we were banished?"

"Oh no, a little farther away from there. I've parked her in the gardens of your castle," he said.

Twilight returned with a bucket. "I've extended the atmospheric shields to encompass the whole garden. We should be fine once we get inside, am I right?"

"Yes, we've created an air bubble over the Maria for our own safety. The air bubble should still be working," Luna said.

Twilight smiled. The Doctor motioned everypony to follow him for the time being. He threw up the doors, and Twilight's eyes couldn't stop expanding. In front of her was a giant castle in a cave. The castle was made of marble and gold with coats of arms all over the place. The coat of arms were decorated with Luna's Moon rising over Equestria with shooting stars surrounding it. The cave they were in was beautifully decorated with a memorial to two alicorns. Their faces could not be recognized since they were blank. One of the alicorns were definitely a male given the body structure. Upon looking at the memorial, Twilight felt her heartstrings plucking. The two looked so sad.

The princess of magic found herself stepping onto the surface of the moon. Immediately she felt the foreign history of Luna's rage build inside her. Her anger and sadness washed over her like a wave. The castle was something to behold. "This is beautiful," she said.

Princess Luna smiled as she approached Twilight. "We tried to outdo our sister since she had our parent's castle. It is a remarkable treasure that we keep intact. One day, we may bring the Lunar Castle to Equestria."

Twilight looked forward to it. The Doctor walked forward with Derpy by his side. "Well then, we can stay here for the time being. We need information on what we are dealing with."

Twilight nodded. The history that this castle had seen may be what she was looking for. What knowledge could be behind those walls? What secrets could-

"Oh, we just forgot. Our sister sent us some of these weird cream-filled cookies during my banishment. I never got to eat them. This time, I will remember to find them!"

Nevermind.

* * *

><p><strong>AN: This chapter was especially long, and I do think I owe you all this. I will get this up and immediately begin working on chapter 10 soon enough. I am going to be focusing more on my personal works for a while so I will be updating soon. Remember to review and answer the questions above. I'd love to hear from you. Until next time, Flutter On!**

**-SirScribe**


	10. Luna remembers

**A/N: Greetings everyone, SirScribe here with another update to **_**Dark Vengeance**_**. I want to thank everyone who reads this story, it means a lot to me that you do so. I think that I should not have such a long opener per chapter since I did so in the last one. I apologize for doing so. I will try to keep the author's note as short as possible.**

**The cast of MLP aren't here right now since they have to get ready for the Equestrian Games coming up. Cheer for the best and keep a watchful eye out, there could be trouble in the Crystal Empire. Anyway, without any more talking, let's get started. I don't own MLP: FiM. All rights go to Hasbro and the creator, Lauren Faust. You go Lauren!**

**ONWARDS!**

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><p>The inside of the castle reminded Twilight of the Canterlot Castle. The architecture was almost an exact replica of Canterlot, now that she thought about it. It would make sense because of how Luna was able to maneuver the elite city without difficulty. The walls were draped with beautiful tapestries with many of the constellations Twilight found incredible. She was being led by the princess of the night, and behind Twilight was the Doctor and Derpy. The pair seemed to be conversing between themselves about random things. Twilight heard some of the words they were exchanging, yet she had to block them out of her mind. There is no way anypony could've had tea with Starswirl.<p>

Twilight looked up towards the ceiling. Pegasi statues with spears stood on support beams. For a single moment, Twilight had to tell herself not to look away. Mainly because she was fascinated by the beauty that went into that work, and the material used to craft it.

"Solid gold," Luna said.

Twilight looked back to the princess. "I'm sorry?"

"The statues are made from solid gold. I found a lot of useful things on this rock during my imprisonment, some of which went into the design of the building," she said.

Twilight nodded. "Wait, how come when you talk, you sound like a more modern pony. You're using the new English!"

Princess Luna looked back at the Doctor. "The ship you were in has something to do with it. The Doctor calls it a 'TARDIS Translation Matrix'. Basically as long as you are near the TARDIS, you can understand any language. I am talking normally, it is you who is speaking in the tongue of old Canterlot," Luna said.

Twilight looked back at the Doctor. "How do you know him? You two seem to know each other well."

"He was there when I needed him. It started when I was banished here…

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><p><em>Luna was in disbelief. For one moment, she had lost control of the powers she learned from Sombra's magical library and the next, she was on the Moon. Her shock turned to anger as she screamed toward the planet below, alas, space was unforgiving. Her voice was confined to her Moon alone. There was no way she was ever going to reach her betraying sister. Luna collapsed on the ground and sobbed.<em>

"_Tis not fair! Tis not fair!" she screamed. "Thy heartless wretch! We are deserving of the throne before thee!"_

_No response came from the planet. She didn't expect it to happen. Luna sighed as she walked away from the planet. She remembered the day it all started. While Celestia and Sombra were fighting, she had stolen into the library and 'checked out' a few spell books and scientific writings. In the books, there spoke of a rare phenomenon where the Moon would cover the Sun, creating darkness across the land. Luna only stole a glimpse of the spell before she fled. Her jealously toward her sister blinded her from the truth._

_Luna looked up from her memories. In front of her was a large cave. She sighed as she had found her new home. She approached the cave, but stopped. Something was inside the cave. Something shiny. Luna galloped inside the cave and found her prize. It was a chunk of gold. She picked it up and studied it carefully. It appeared to be part of something bigger. She looked around and discovered a mine shaft in the wall. When she entered, her eyes never went wider. She had a way to survive._

_Over the next few months, Luna was hard at work building her new home. If she wasn't going to rule Equestria, she was going to rule space. She commanded the stars, so she was going to reign over her sister. With the minerals inside the Moon, Luna was able to construct a castle, mainly from gold and quartz. The body of the castle was complete, but if Luna were to reign, she would need a throne, servants, and a beautiful garden in the back. Summoning Shadow Ponies, Luna put them to work. Some had descended to the planet to steal more supplies. Today, ponies remember them of being supernatural monsters. In a way, Nightmare Moon was still alive in Equestria._

_With the castle complete, Luna sat proud at her new throne. Her victory was short-lived, however, as reality settled in. She was sent to prison, and she built the world's largest prison cell. She wasn't royalty. She skulked around her castle, hoping something could happen. She looked down to the planet and wished to return. She tried screaming to her sister, begging her to reconsider._

_300 years passed before Luna accepted her situation. She awoke from her sleep every day and explored her Moon. The mine shaft she found on her first day provided more than she expected. She found more jewels, magical artifacts, and even an underwater basin. She spent more of her time swimming and building from the jewels. The magical artifacts gave her the freedom to experiment just as Starswirl used to do. She was her own wizard._

_One day, as Luna sat in her empty throne room reading an old poem she wrote, she heard a sound echoing through the halls of the castle. A _whirrrrrr_'ing sound it was. Luna was confused, and with confusion followed curiosity. She explored her castle once more, occasionally running through her servants. She threw up the doors leading to her balcony, and was at a loss of words. On the edge of the balcony was a blue box. A simple blue box with a light on the top. The box appeared to have doors, and before she could get close to it, they opened. Inside was a brown stallion and a pegasus. They both looked at her with curiosity. The pegasus approached her slowly._

"_Doctor, is that—?"_

"_I believe so Derpy. It's her."_

_Luna was in shock. These ponies knew her name? She approached the two. "Um, welcome to our Moon. I be Princess Luna, and who art thou?"_

_The stallion was the first to speak. "I'm the Doctor, and this is Derpy Hooves. We were just passing through."_

_The pegasus, Derpy, looked back at the stallion. "Doctor! We just met Princess Luna during her banishment, and you want to leave already?"_

"_Being here is bad enough. We could very well have given Nightmare Moon a way to escape," he said._

_Luna was heartbroken. "Please, if it pleases thee, would'st thou like a cuppa tea?"_

_The Doctor's ears perked up. "Tea sounds nice. Thank you."_

_The Doctor closed the door behind him and locked the door. He noticed Luna looking at him. "It's a habit of mine. I always have to lock the door before I leave."_

_Luna nodded and showed the two to her dinning room._

_As it turns out, the Doctor and Derpy were there a good 5 days. The three of them shared laughs and tears as time went on without the Time Lord. Derpy was playing 'Keepaway' with the Shadow Ponies while the Doctor and Luna talked. When the time was up for them, Luna was beginning to feel heartbroken, but her luck changed for the better._

"_Would you like to come with us?" the Doctor asked._

_Princess Luna was overthrilled. She agreed and entered the Doctor's mysterious blue box. Since Luna's imprisonment was never recorded in the present, she was free to go anywhere but back to Equestria. As long as Nightmare Moon's shadow stayed on the Moon, nopony would notice when the Princess of the Night disappeared._

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><p>"—and when we returned, the stars were forcing me to turn back to Nightmare Moon. The Doctor and Derpy had already left when they knew the time. They told me to hang on and never let anger consume me like last time. The next thing I know, Celestia was standing in front of me. That was the night you used the Elements."<p>

Twilight smiled back at the Doctor. "He was your hero."

"Oh yes. We traveled everywhere and anywhere. Since I had no timeline on the Moon, I could return at any date in history. He brought me back on the 1000th year, and that's when my timeline continued. We did a lot during our travels, but there are some things I would not like to remember."

"Like what?"

The Doctor stepped in. "We were on the planet Raxcarlificus in the year 4,690, and there are strict rules when it comes to companions. See, there are no 'friends' on the planet, just, um, lovers."

"Derpy and I faked marriage with the Doctor to avoid prosecution," Luna said, hiding her face behind her hoof.

Twilight resisted laughing. "We managed to fool the government, but I discovered that I've never kissed a stallion before, and I ended up kissing his mane. It was humiliating."

"You three get a fake divorce afterwards?"

The Doctor sighed. "Very funny."

Twilight smiled and they all continued walking through the halls.

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><p><strong>AN: I hope you all liked it. I will be back sometime next week for the continuation of _Dark Vengeance_, so hang on! Season 4 is ending quickly, and I think that this season finale will be so awesome! Until next time**

**-SirScribe**


	11. BRAINSTORM!

**A/N: Greetings everyone, and welcome back to **_**Dark Vengeance. **_**I hope you all had a good week. With some spare time in between classes, I will be able to focus more on Fanfiction without worrying about that extra homework assignment and test. Now I can worry about the test that I probably bombed because of some late night reviewing. Yeah, not my best idea in the universe. Anyway, I'm back and more than likely updating the **_**Starswirl's nightmare**_** after this. I am also planning some one shots for the future. Let's see what is ready.**

**UPDATE: I am in the works on designing another OC story with… an alicorn. I know the first rule of OC's is 'Don't make an alicorn OC', but I want to change that. I'm trying not to make him too powerful and with a rocky backstory. It will be some time before I publish it, but it will exist. I know what NOT to do when making this OC, so don't expect it to be the shadow emperor of Equestria and married to each of the Mane 6. That is just horrible. Anyway, onwards!**

**Disclaimer: I don't own MLP:FiM. All rights go to Lauren Faust and Hasbro.**

**ON WITH THE SHOW!**

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><p>The large doors flew open, exposing the ponies to the greatest library in the universe. During the 300 years of isolation, Luna had read almost every single book created during her banishment. Thanks to her Shadow Ponies, she was quite entertained with some marvelous works of art. Some of those works were made to live by Luna's extensive research of dark magic. The characters in some of her books only lived for a short amount of time, however, but they were companionship.<p>

Twilight's eyes widened as she drank in the library. There were 3 stories full of books, all neatly assorted by name and decade written. In one level alone, Twilight could read a centuries worth of marvelous works. To her, history was preserved in Luna's library.

The Doctor looked amused. "Still trying to top my library?" he asked.

"Please Doctor, this is a book store compared to yours. You have the complete works of many great unicorns in your library, but I have the most famous collection," Luna said.

The Doctor nodded. "The Complete Works of Starswirl the Bearded are a great collection. You beat me in getting those," he said.

Twilight spun around. "You have the Complete Works of Starswirl the Bearded?"

"All 256 volumes, including 10 out of the 12 Missing Star Scrolls. Those are extra."

Twilight's jaw dropped to the floor. "Right then, we need information on how we can defeat those 4 below, and with Twilight's broken Element of Harmony, that will be difficult to find. We might as well get started," the Doctor said.

The four ponies nodded to each other and went their separate ways. Twilight flew all the way to the top of the library while the Doctor and Derpy stayed on the ground levels. Luna smiled at how she remembered seeing the Doctor and Derpy for the first time. She remembered how they were amazed with her library, even though half of it was still incomplete. She remembered when they both ran around and reading through her extensive collection. She sighed as she flew to the top to help Twilight.

* * *

><p>As time went on, the 4 ponies found nothing to help them defeat Sombra and his allies on the planet below. Every book they found were either storybooks, autobiographies, of fact books surrounding the Elements of Harmony. With the Elements out of order, there was no way a story about a mare who lost a horseshoe will help them with anything. Twilight had no idea what to look for. The Doctor and Derpy left the library while Luna stayed behind with Twilight.<p>

Speaking of the lavender alicorn, Twilight was perched high in the library with three books open to her. She sighed heavily as she found nothing in them. All she found were journals left behind by some of Equestria's best authors. She replaced the books in frustration. Luna sighed as she flew up to the princess of magic.

"Still can't find anything?" Luna asked.

Twilight sighed. "It's like the Elements appeared out of nowhere. There is no manual into working the Elements, there is no history of the Element's beginning, and there is nothing about what to do when an Element breaks. There is also nothing more powerful than the Elements. How are we going to defeat Sombra?"

Luna placed her hoof on Twilight's shoulder. "Calm yourself, Princess Twilight. You've handled worse problems before, and I have faith you will find the answer soon," Luna said.

"But ever since Canterlot, it seems as though my thinking has been shut off. I can't think anymore. I think that Equestria is no longer in my hooves. I think the Doctor should save us because I have no idea how to fix this," she said.

Luna sighed. "How many times has he saved us before?" Twilight asked.

"Oh many times Twilight. He saved us from so many evil things that even I or Celestia could no fight. Enemies who have knocked on our front door were greeted by the Doctor, and I've seen him do it. There are many wonderful things about the Doctor, but he is not a god. He cannot do anything all by himself. He needs help and he relies on his friends to help him. You are very much like him Twilight. You both have a problem that cannot be solved alone. It will take the both of you to save us all."

Twilight smiled. They both flew down to the ground and followed the Doctor and Derpy to the kitchen. They entered to find the Doctor scrambling around, gathering ingredients from Luna's cabinets. He hoisted a bag of flour on his back and ran as Derpy was busy reading a recipe book. She was wearing a chef's hat and apron.

"Eggs?" she called out.

"They're here!"

"Milk?"

"You're sitting on the carton," the Doctor said.

Derpy looked down and grabbed the milk. "And finally flour?"

"Right here!" The Doctor heaved the bag on the table.

Derpy smiled. "Yay, now I can make us all a good breakfast. I will be ready soon," she said.

The Doctor smiled and turned to Luna and Twilight. "She has used every single ingredient in my TARDIS and now she's hungry. I probably should've stocked up beforehoof," he said.

Luna smiled. "She did make the best muffins. I miss her cooking."

"Oi, I cooked as well when we picked you up!"

"I don't like eating coal, Doctor," Luna said.

The Doctor smirked. "Anyway, you girls find anything that we can use?"

Twilight shook her head. "Not a single bit of information that isn't news. I've studied many different sources of the Elements and they all say nothing on how to fix them. I wish we had a clear idea what to do so we can do it," she said.

Luna shrugged. "I released all the information that I know about the Elements. When Discord was once ruling Equestria, we found the Elements inside a chest from the wreckage of an old ship. We figured that they were from a distant land."

Only the Doctor caught her lie. He was the one who told Luna where to look for the Elements the first time around. She was holding back something important about the Tree, but he didn't ask any questions. If Luna hasn't said anything to her, then he shouldn't. "That doesn't help us much. We can't guess where the chest came from. It's as if the Elements just spawned into creation," she said.

The Doctor sighed as well. Suddenly, they heard the sound of wood falling to the floor. They all turned around to see Derpy standing there with a hoof with batter. Her wooden spoon was on the floor. Her eyes seemed to be focused in one direction. Derpy was looking at what was behind the trio: a sandy colored wolf. The wolf was looking at her with curiosity in its eyes. Derpy felt something racing inside her as she continued to stare at the wolf.

The Doctor moved forward. "Um, Derpy?"

Derpy turned to him. "The Elements are like family: they care for each other," she said.

The three were confused at Derpy's comment. Once she said that, she felt limp and collapsed. Luckily the Doctor was there to catch her. Twilight looked behind her, and saw nothing. There was no wolf at the spot where Derpy was staring at.

"Derpy? Derpy?" he called out.

Derpy's eyes opened and they were as wall-eyed as usual. "Hi Doctor! Did I fall?"

The Doctor chuckled. "No Derpy, you just slipped on some of the batter, that's all. Lucky me I was there to catch you."

Derpy chuckled as she sat up right. Twilight moved forward and tried staring into her eyes. "You seem like yourself, but you weren't earlier. I wonder what got you so upset," she said.

"What do you mean?"

"You said something earlier. Something about the Elements being like f—"

Suddenly, Twilight's mind exploded. A thousand thoughts raced through her mind faster than any other idea before her. Without saying another word, she bolted out of the kitchen and towards the library. The 3 baffled ponies only followed her. When Twilight entered the library, she flew up to the top of the room and grabbed 3 books. Each one was a book written by Starswirl the Bearded. She flew back and threw one of the books open.

The Doctor looked up at Twilight, and what seemed like a second later, he understood what she was thinking.

"The Elements are family!" Twilight said.

"We know Twilight, Derpy told us that," Luna said.

"And she's right!" Twilight shoved a book in the lunar princess's face. "Starswirl studied the Elements while you and Celestia had them. After what took years to figure out, he came up with the ultimate theory about the Elements!"

"And that is?"

"They're family. This is Starswirl's hoofnote on the subject." Twilight removed the two papers and began reading:

_On the 15__th__ day of the Cycle of Winter, I have discovered a peculiar fact about the Elements of Harmony: they are alive. These Elements are what has brought Equestria to peace numerous times already, yet I wondered how they can retain all that power they eat up. 2 nights ago, I came across the Elements 'praying'. Their energy signatures were sky rocketing and pulsing, like the actions of a pony's heart. This led me to experiment on these gems, and there is so much to them than I once believed. These Elements have the power to replenish themselves after every attack almost immediately as long as they are together._

_The Elements are alive even as I write this hoofnote. I will continue my studies on the matter and return for a full update._

Twilight looked up. "They're alive. The Elements of Harmony are alive!" she exclaimed.

Luna looked back at the book. "There's another hoofnote, but it appears as though Starswirl was panicking," she said.

Twilight looked back at the book. Indeed the writing looked rushed. Before Twilight had a chance to read it, the Doctor stole the book away. Twilight jumped as he abruptly slammed the book shut and hid it away. Luna looked at him, stunned. The Doctor didn't say anything about the book. The princess of magic was only able to get a glance at 3 words in the hoofnote: _Elements of Disaster._

Derpy sighed. "So if the Elements are alive, should we help them?"

"Yes, and we can do that. Princess Luna told me about the Discord incident a few years ago. From what I understand, Discord targeted the Elements because he knew that without them, he can cause as much chaos he can without anypony stopping him, right?"

Twilight nodded. "And if it took all 6 of you to fully restore their power, it will take 6 of you to mend the Element of Magic."

"We can find my friends! We can repair the Elements!"

"And Discord will have a reason to worry. If we can cause an uprising in surrounding towns, like Ponyville, all their attention will be geared towards the resistance instead of us. We can find your friends and find the Elements at the same time!" The Doctor was grinning like the mad pony he was.

Luna stepped forward. "Doctor, we must have a clear idea about the location of the Elements. They could be anywhere in Equestria," she said.

"Yes, but they would have to be nearby just in case something goes wrong. Their power is enough to cast darkness all over Equestria a thousand times over. The Elements are Sombra's only Ace. If we can take them away, and you powering them up against the 4, Sombra will be fully defeated," the Doctor said.

The four ponies smiled. "Right then, we're off!"

"It's time to take Equestria back!" Luna proclaimed.

"Oh yes! Allons-y!"

The four ponies dashed out of the library and into the gardens. The Doctor blew past the doors, and once everypony was in, released the brakes on the TARDIS console. The room began rocking back and forth at the TARDIS dematerialized from the Moon.

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><p><strong>AN: I hope you have liked this addition to **_**Dark Vengeance**_**. Leave a review, and I will get back to you as soon as possible. The season finally is near, and it is time to unravel the mystery behind the Chest of Harmony. (I'm so calling it that now). Anyway, Keep Calm and Flutter On!**

**-SirScribe**


	12. The welcoming committee

**A/N: Greetings everypony and welcome back to **_**Dark Vengeance.**_** Please excuse me from my absence for it was getting hectic over here in college. With finals coming up and my grades far from decent, I needed to decide what was more important, so I had to take a break. I know that sounds wrong, but it had to be done. I'm being honest here. Anyway, while on my hiatus, I began thinking up how I want to finish this story, and I began writing the final chapter. One has to know how to end a written work in order to begin. Anyway, once I have it all set up and worked with the storyline, I will have it uploaded. Remember that reviews are a perfect way to show support for this and other stories. Let's get started.**

**Since the Mane 6 are resting from the season finale (Which Rainbow hinted about a few chapters back), I'm alone in the studio. Watching that finale was like watching Dragon Ball Z back when I watched the hell out of it. I am hearing that the next season won't be out until next year. I hope that's just a ploy to catch us off guard. It better be a great season premiere if we have to wait a year. Anyway, I don't own MLP: FiM. All rights go to Hasbro, Queen Lauren Faust, and anyone else who owns MLP. Onwards!**

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><p>The control room began rocking back in forth, throwing Twilight's stomach into every twist and knot in creation. If she lost her lunch in the TARDIS, would the Doctor forgive her? She was about to find out when Luna gave her a bucket.<p>

They had left the Moon a while ago, and with some piece of equipment that the Doctor had, they were on their way to finding one of Twilight's friends. The Doctor amazed the princess of Magic even more when he revealed what he was. A Time Lord? Such a name was only mentioned in myths and storybooks that pre-date Celestia's Reign. A race of beings who had a near unlimited supply of knowledge and power, and with a civilization that lasted billions of years. The name 'Doctor' was never mentioned in any of the books she read about this race, but if he was in it, he would be everywhere. He talked quite a bit about his race before, but Twilight noticed that once he was done talking about them, he would stare into nothing like he was sad.

The Doctor pulled on the brakes. "We are back in Equestria," he said.

Luna smiled. "And they don't know?"

"No. I had the engines on silent and have her in camouflage mode. We cannot be detected by any sort of magic. I guess that would've helped us get past the Shadow Ponies earlier, but where's the fun in that?"

Twilight face-hoofed. The Doctor better be smarter than he is letting on. Her eyes scanned the control panel in front of her. Somehow, this disorganized series of panels provided the best way of navigating between the Moon and Equestria. On the control panel next to the Doctor was the book he snatched from her back in Luna's library. A hoofnote left by Starswirl was somehow forbidden to her. It was like he and the Doctor know something that shouldn't be shared. A secret concerning the Elements.

The Doctor stretched his neck. "Come along Ditzy, we need to find your friend. Rainbow Dash, right?"

Ditzy nodded. "Okay, I got a trace of her in the Everfree, and with what you all said about that place, I have a reason to believe that she may be in danger. We find her before anything else does," the Doctor said.

"Our friend Zecora lives here. Maybe she can help us," Twilight said.

"The zebra from Nightmare Night a few years ago?" Luna asked.

Twilight nodded. "We remember that night perfectly."

The princess of magic chuckled nervously. She wanted to forget that night. "Where does your friend live?"

"In the center of the forest. There is a grove of Poison Joke not far from her hut. Let's find Rainbow first."

The Doctor opened the doors. They landed in a clearing somewhere in the forest. Everything would've been fine, but since Nightmare defeated Celestia, the Moon was high in the air, and it appeared to not have moved at all since their escape. "This place hasn't changed since I last saw Starswirl," the Doctor said.

Twilight scoffed. "You cannot have me Starswirl. Time travel may be possible, but I can only go back about a week," Twilight said.

"Well I have, and we even went exploring around here. We went down that bog once and found a basilisk. Sucker was huge."

"I remember that basilisk! Celestia and I would throw stones at it whenever it got close to the castle," Luna said.

"Yeah, I remember it saying that all you had to do was ask it to go somewhere else. It was tired of the stones."

"It was a nice time seeing Starswirl," Ditzy said.

The Doctor smiled. "I can understand you seeing Starswirl Luna, but you Doctor? I can't see you and Starswirl talking," Twilight said.

"We do more than talk. Ditzy often trades recipes with him while I battle at chess," the Doctor. "He always cheats."

"I warned you," Luna said.

"His muffins were amazing. Too bad I lost the recipe."

The Doctor placed a hoof on Ditzy's shoulder. "I have it memorized. We can write it down later so you have a copy."

"Yay!"

Suddenly, there was a loud crunch. The four ponies stopped in their tracks. They were in a thick brush. Twilight and Luna stood ready to defend. The Doctor and Ditzy were still. "What was that?" Ditzy asked.

"Maybe somepony is following us. That sounded big though so I don't know," Luna said.

A loud roar blasted through the forest, hitting the four. Twilight knew that roar very well. Too well. Before she had time to speak, the trees surrounding her came crashing down. From beyond the bushes, the Timberwolves leaped out. Ditzy and Twilight screamed while Luna charged her horn. She fired a magic blast, scattering the branches of the Timberwolf. Four more began running at them from behind. Without a second thought, the four ran. They jumped out of the brush and into a clearing.

Twilight looked behind her. The Timberwolves were getting closer. She fired a magic blast, but missed the leading Timberwolf. She turned and continued running. She noticed the Doctor was trying to run on three hooves as he was fidgeting with a silver stick. The stick had a blue tip on the end. He growled and cursed about not having hands. Twilight understood that term.

"What is that?" Twilight asked.

"It's a screwdriver," he responded.

"That is not a screwdriver. That looks like a tiny flashlight."

The Doctor chuckled. "Looks can be deceiving, can they? Ugh, Ditzy, you have open hooves, can you switch it to Setting 496?"

Ditzy nodded and flew up in the air with the screwdriver. "What, are you going to build a cabinet to throw at them?"

"No! Setting 496 is Molecular Depression. By releasing a sonic wave at the ground beneath the Timberwolves, I can cause the ground to weaken and depress beneath them, creating a hole. Have you got it yet?"

Ditzy fumbled with the device. "Got it!"

"Good, now press the button, and—"

Ditzy pressed the button, but she didn't aim. The sonic wave was aimed at the hooves of her friends. The ground beneath them weakened and all three fell down the hole. "Ditzy!"

The pegasus blushed. "Whoops, my bad." She readjusted the device, and pressed the button. This time, the ground underneath the Timberwolves collapsed, sending them all into the ground. Ditzy looked over and dropped the device into the Doctor's hooves.

"Ok, that should take care of everything for a little while. Ditzy, a little help?"

The pegasus flew down to help the Doctor. Meanwhile, Luna had to carry Twilight due to her injured wings. She never realized how much she relied on them until she was injured. She felt like a regular unicorn again. The four touched hooves onto the ground and turned to survey Ditzy's work. She was still blushing from her mistake, but the Doctor didn't mind. "What is that thing?"

"A Sonic Screwdriver. Think of it as a little bit of the TARDIS. My most faithful of gadgets that have well over an infinite amount of applications," the Doctor said. "I love this thing."

"Don't let my sister in law hear you say that," Twilight said. A second later, her eyes bulged. "Wait a minute, Cadence! The Crystal Empire!"

Luna's alarm went off. "I'm sure Princess Cadence is fine. Right now, we need to focus on finding your friends. Where is this Rainbow Dash?"

Upon saying the pegasus's name, a loud roar echoed through the forest. The Timberwolves had returned, but they carried an aura of dark magic. Luna tried firing a spell at them, but it bounced off and flew into the forest. The princess of the night gulped. Without another word, the four high-tailed it into the forest. Behind them, the Timberwolves howled before commencing the chase. The Doctor tossed up the Sonic Screwdriver to Ditzy. With Setting 496 already programmed, the wall-eyed pegasus began firing. Unfortunately for the 4, the Timberwolves were smarter than the others. They leaped out from the holes the second they fell in. They were even smart enough to evade the traps altogether.

Luna led the group around a sharp corner, and kicked a boulder into the path of the Timberwolves. The boulder was smashed into dust instead of breaking the Timberwolf structure. The four continued to run, but found themselves at a dead-end. In front of them was a cliff, and with two ponies who couldn't fly, the chances of escape seemed to be slipping away. The turned back to face the Timberwolves.

The predators stopped, completely sealing their lunch in. They slowly approached the four, and before death could great them, one of the Timberwolves exploded in a green dust. The last thing they all heard was a small yelp from it. The four looked around, and noticed a pegasus in the trees with saddlebags filled with bottles. Twilight couldn't make out what was in them, but she guess that they were potions. The Timberwolves growled at the pony.

"You want to hurt my friends, you're going to have to get through me you pile of firewood!" yelled the pony.

Instantly Twilight knew who it was. The pegasus leaped into the air and threw some more bottles at the Timberwolves. Two exploded while another opened its jaw to swallow it. The potion exploded, but did nothing to the wolf. The pegasus got into the Timberwolf's face, kicked it with its back legs, and flew off. The Timberwolf quickly followed the pegasus. A few minutes passed by before they heard a yelp and a crash. The crash seemed to have been made by a falling tree.

Silence filled the forest. The ponies stared into the thick brush, expecting something to happen. Indeed something did. From out of the darkness of the Everfree Forest, a pegasus came flying at them. She seemed to be carrying something in her hooves. The pegasus came into full view and dropped whatever was in her hooves. A pile of wood. Twilight smiled. "Poison Joke?"

"I guess there are good things that come out of being an egghead," Rainbow Dash said. Without another word, the cyan pegasus tackled Twilight. The princess yelped in pain as her friend trapped her in a bear hug. "We thought you were dead!"

Twilight sighed as she wrapped her hooves around her friend. "I thought that too. Thank Luna for being a great cushion to break my fall."

* * *

><p><strong>AN: Well there you go. Sorry for taking so long to update. I will try to update frequently from now on. Now, we wait for season 5. Have a great day and I will catch you later.**

**-SirScribe**


	13. Zecora and Rainbow Dash

**A/N: Haha, the fun has been doubled!**

**Greetings everypony, I know that I was on hiatus for a long time, but I thought I would make it up to you by updating two chapters in this story. I hope you all are having an absolutely fantastic morning/afternoon/night. It feels good to be back at my craft. I've been working on a chronicle for after the timeline of **_**Dark **_**Vengeance, and I think I have it down. This story is about halfway done, and the next installment will be available soon. I'm also working on some new stories outside this timeline so be ready for that. Um, and I may start working on the OC story that is mentioned in my first Fanfic, **_**New Life in Ponyville.**_** Anyway, let's get this party started!**

**Pinkie: PARTY!**

**Rarity: Pinkie please, not so loud**

**Me: Presenting Pinkie and Ms. Rarity from Ponyville.**

**Rarity: Charmed to be here. When Pinkie would tell us about this whole other world where we are the subject to a series to 'cartoony' antics that are documented and dispersed for complete strangers to watch and laugh with, I was nervous on coming here.**

**Pinkie: It could be worse**

**Rarity: What could be worse than finding out that your whole life has been publically exposed and you had no idea?**

**Me: Be glad there is no internet in Ponyville. Anyway, let's rock. Rarity, care to do the honors?**

**Rarity: Gladly. SirScribe does not own MLP:FiM. All characters, situations, mythical objects, and storylines all belong to Lauren Faust and Hasbro Animation Studios. SirScribe also does not own Doctor Who, TARDIS, or the Sonic Screwdriver. Doctor Who is owned by BBC.**

**Me: I think that was the longest disclaimer I've ever had on here. Anyway, let's roll!**

**(I mean no offense to anyone who takes MLP to the second level on the Internet. You know who you are)**

**ONWARDS!**

* * *

><p>The 5 ponies began walking through the forest. Twilight and Rainbow led the group through with no way to stop. Twilight told Rainbow all about what had happened after she woke up, including being sent to the Moon, reading Starswirl's own hoofnotes, the TARDIS, and pretty much everything else in between. She also told her about her handicap of not being able to fly. Rainbow sighed as they continued walking.<p>

"I guess I'm going to have to teach you how to fly again, huh?"

Twilight sighed. "I guess so, and I was getting good at it. So what's happened since we last saw each other?"

Rainbow stopped midflight. "Everything went wrong back in Canterlot. Sombra sent Pinkie and Fluttershy to the dungeons with Princess Celestia. She didn't look so good with her broken horn and Pinkie had not said a word. Her mane went flat as they carried her away. I couldn't stop them with my wings. They got rid of me before I had a chance to escape. I was plopped out here in the middle of the forest, and I thought I was going to die, but Zecora found me. She lifted the curse off my wings and I've been here ever since. It's been tough out here, especially with the Forest retaliating."

"What do you mean?"

"Zecora said that for a while, the Everfree Forest started fighting. She's seen plants move and the mist from within get thicker. She says something is coming."

"How long have you been here?" the Doctor asked.

Rainbow looked over. "Who are you?"

"I'm the Doctor," he said.

Rainbow raised an eyebrow. "Doctor who?"

"Just 'the Doctor'. I helped nurse Twilight back to health, but it was Luna who saved her," he said. "And I'm sure you know my faithful assistant, Ditzy."

Ditzy looked over at Rainbow. They touched hooved and laughed. "So this is where you fly off to after your mail runs: off with your coltfriend."

Ditzy's face turned bright red. "He's not my coltfriend. We're just friends that's all," she said.

"Uh huh, sure and Twilight didn't have a small crush on that guard in the Crystal Empire."

"Can we stop talking about Flash already? He is just a version of a guy I met while in the other world, that's all he is to me. There was no crushing and no flirting so quit it!" Twilight barked.

Rainbow laughed. "Oh c'mon Twi, you know I'm pulling your tail. Seriously though, you did."

Twilight made a move to grab Rainbow Dash, but she only elevated a few more feet off the ground. She scowled at the pegasus. "Show some interest with a male for half a second and I never hear the end of it. First Rarity tries to set me up with him and now he is being used against me. Brilliant," she muttered.

The ponies continued walking through the forest, eventually finding the hut of Zecora the Zebra. Rainbow knocked a few times on the door before entering. Everything on the shelves looked exactly the same as the last time Twilight was here. The creepy masks that followed her every step were still hung from the ceiling as a security system. That is probably one reason why nopony tries to enter without her permission. Those masks probably can speak.

Bottles of variously colored liquids lined the shelves. Potions that ranged from simple healing spells to complex incendiary spells and Transfiguration. Twilight had the displeasure of trying a Transfiguration potion once. She often wondered the life of a dog, and when she got it, she was happy to be a unicorn again.

In the middle of the room, right next to a giant cauldron of a green liquid, stood the zebra herself. She was muttering an incantation in her native tongue, but when Rainbow landed on the floor, she stopped and turned. She looked weary like she was working non-stop since the invasion.

"Please Rainbow Dash, if you will come in, please be as silent as a falling pin," she said.

"Hehe, sorry Zecora, but I found Twilight and some new friends of hers."

Zecora turned to greet the new friends of Twilight, but when her eyes rested on the Doctor's, she smiled. "My eyes deceive, it is the Doctor. So long have I waited to enter my front door," she said.

The zebra inched closer to the Time Lord. "You've seen me before?"

"And I fear we will meet some more. Please sit and you will see, there is much to fear in this monstrosity."

The ponies all glanced at each other before approaching the cauldron. The liquid bubbled from the flame, and before Twilight knew it, an image popped up inside the liquid. She recognized it immediately as the Crystal Empire. From her last vision, Sombra was near victorious against Cadence. The Empire looked dark and sad. The Crystal Ponies were all chained up and forced to and from the mines. The palace was surrounded by living shadows and changelings.

Twilight focused more into the image. Underneath the palace was the podium for the Crystal Heart, but something about it was different. It wasn't spinning like it used to. Instead, the Heart was motionless and dark, like all of the happiness and love that was inside was suddenly gone. The surface was cracked like a broken heart is normally depicted.

"Dear Celestia, he won," Rainbow said.

"I've seen something like this before. He may have won, but the war isn't over yet. They still don't have it," the Doctor said.

"Have what?" Twilight asked.

Ditzy and the Doctor exchanged looks. They knew about the artifact she would later find. The Tree and the gift inside. Twilight looked closer into the image, and noticed a familiar pony standing beside the Heart. A unicorn with purple curls in her mane and a crystalized military uniform. It was Rarity guarding the Heart. Her eyes still green from the dark magic used against her.

"Rarity."

Zecora nodded. "Dark in mind as her heart, setting her free will play a major part."

Twilight nodded. "What can we do?"

Zecora put a hoof under her chin. "The answer be a holy key, so where is your Element of Harmony?"

She hung her head. "Broken, but I think we can make it right. We need the Elements to restore it," she said.

Zecora nodded. "That be done is the easy path, but what happens now against the dark's wrath?"

"Well, we need to cause a revolution. Something to keep Sombra and his goons distracted, but what can we do?"

"Better not to flee, you may need the Harmony—"

"Free. Harmony free," the Doctor interrupted. "We must free the agents of Harmony, meaning your friends."

Zecora glared at the Doctor. "Perhaps another to please your aching heart, but be warned it is one difficult part. A dark lord's death is the key, to rid us all of the Unholy Trinity."

That last line directed to the Doctor. "But, there's 4 of them," Ditzy said.

The zebra looked over. "I know what I said and I said what I meant, now it's time to sleep your day is well spent."

At that point, Twilight yawned as did everypony else. They all found themselves quietly walking away into some empty cots. Within seconds, all but Twilight were sound asleep. From beyond her fight to sleep, Twilight seemed to overhear an argument between Zecora and the Doctor.

"Interrupt me and make false words, surely your mind has gone to the birds!"

"I know a lot about your magic in potions, including prophecy, but the tree cannot be known. It isn't time."

"'Time is not the boss' are those your words, or have you lied you ungrateful curd?!"

"I need this timeline to progress as slowly as it can. We can win, but without ancient magic. Without the tree."

"Very well Time Lord I will remember, but now is your time to slumber?"

"Not yet. I'm not ready."

Twilight fell asleep with a tree in her mind. Tomorrow, the revolution begins.

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><p><strong>AN: Well everypony, I hope that was good for you. Rhyming with Zecora is impossible, but I tried to make it work. I'm trying to make this work in between seasons 3 and 4. Hopefully it will work out. Anyway, enjoy your time and I will catch you later!**

**-SirScribe**


	14. Sombra and Discord

**A/N: Greetings ponies and humans, SirScribe here and I'm dishing out chapter 14 of **_**Dark Vengeance!**_** I love reading the reviews because I know you are following this story to its end, and it is drawing near. I recently got a job so I have a schedule once again, but it won't be as tough as before with college. Year 1 was recently complete and it is time to rest. Let's get this on, but first:**

**To Just Call Me J: Rarity is the first to be freed and then Applejack. I hope you like these rescues, especially Applejack's. I am an Applejack supporter and I feel what she feels in the fandom. With bronies calling her a background pony and a lesser important Element of friendship, it gets hard to be supportive of a lot of bronies. Honesty is what really makes friendship and harmony because lies and deception are what create chaos.**

**Applejack: Aw shucks thanks sugarcube**

**Me: Ladies and Gentlemen, Applejack**

**Applejack: So ya spend yer free time writin' here but not working on the farm like yer supposed to?**

**Me: Hehe, sorry boss. Anyway, thank you for being here. Without further ado, let's rock. Will you do the honors?**

**Applejack: Nope**

**Me: …**

**Applejack: Kiddin'. SirScribe doesn't own MLP. All rights go to that major fancy HASBRO and Lauren Faust. Doctor Who is owned by BBC**

**Me: Thank you. Now then**

**ONWARDS!**

**Applejack: YEWW HAW!**

* * *

><p>Sombra levitated a crystal to his mouth. With a snap of his jaw, he took a big bite out of it. The taste of crystals, normally reserved for dragons and crazy ponies, felt blissful to the dictator. With the Crystal Empire back under his control, he felt like he could kick his hooves up and finally feel like a king. That included working his subjects to the point of death. He sat in his throne and expanded his mind thanks to the dark magic. He saw his ponies working underground, making him richer by the second.<p>

As he ate his crystal and watched his subjects work, the rest of the Crystal Empire walked and breathed dark magic. Shadow Ponies stood guard outside his castle, ready to defend should there be a reason to do so. His financial advisor stood by his side with a scroll in front of him. As he read the daily report, Sombra tried his best to think above the pony's voice. He hated the daily report. If taping somepony's mouth shut and setting it on fire were looked upon as good, he would be doing that to anypony who talked to him.

"-5 million bits in value in the one hour alone, leading to a combined total of 35 million bits of jewels during this cycle. Congratulations, Your Majesty, you are the richest stallion in Equestria," the pony finished.

Sombra sighed. "These crystals are not to be sold to Nightmare Moon! These are all my jewels and my crystals, not hers! I make one deal with a trickster and I end up losing more than I hoped to gain! When am I going to get what's mine?!"

The pony didn't dare answer. "Leave!"

The pony dropped the scroll and ran out of the throne room. Sombra threw his half-eaten crystal at his advisor, but ended up hitting the door as it slammed shut. He sighed as he pulled out another crystal and began eating. "Stupid equines."

One of the guards spoke up. "With all due respect sir, you—"

"Finish that sentence and you will spend the rest of your days as a chew toy for Cerberus," Sombra threatened.

He shut up immediately. "I want this cycle to feel good to me. Let's take a piece of the Griffon Territories. Which territory is available for us to capture?"

Another guard approached Sombra with a map. He unraveled it, showing the Crystal Empire, the Frozen North, and somewhere in the West, the Griffon Kingdoms. Sombra sighed. The Griffons were once very much closer to them the last time he looked upon the map. "Their wing power is great, but have no magical defenses, correct?"

"Yes sir!"

"We cannot fly unless we have heavy armor, and that can be made using the crystals, correct?"

"Yes sir!"

Sombra studied the map. "We move on the coast, running along the North. The Griffon Kingdom will have impenetrable defenses, but that can be easily taken down by dark magic. While we are there, we can probably just take the Griffons as a whole. Contact Nightmare and Chrysalis and get them to send troops up here."

The guard looked uneasy. "If I may add, sir, that is impossible. Chrysalis is taking the dragons in the South and Nightmare is handling a rebellion that started in Ponyville. We are stretched sir. With the constant weather storms in the North, Shadow Ponies would find it hard to keep their form, and Changelings would not be able to fly. A naval invasion would be best," he said.

Sombra looked over. "Were you a military officer before?"

"Yes sir!"

"Well then, how about this: I send you out there with a spear and a target painted on your back. If the cold doesn't get you, the griffons will."

The guard gulped. "Next time you object to my master plan, I will not give you a fair warning. Contact Nightmare and Chrysalis before I have you obliterated!"

The guard yelped and ran out the door. He managed to trip as he did so. Sombra sighed. There was nopony that served him more than Rarity, and he hypnotized her to be his general. At that moment, the guard came running back. Sombra spit out a piece of the crystal. "Your Majesty! A strange object is flying towards the Empire."

"That is not a nice way of describing Nightmare," Sombra said with a slight chuckle.

The guard stopped. "No sir, um, the object appears to be in the shape of a box, sir! A big and blue box."

Sombra's ears perked up. "What? Show me!"

The guard levitated a pair of binoculars towards the king. He looked out the window and saw the object. It was blue and it was headed their way. He grumbled to himself. "It's probably Discord playing a game with us."

At that moment, a loud BANG! echoed through the castle. Sombra turned around to see Discord in a weird looking hat. It looked like Pinkie Pie's head. Of course it really wasn't, but the god of Chaos was wearing a hat inspired by an annoying baker. He was laughing, oblivious to what had happened.

"—and I said 'Oatmeal? Are you crazy?!' and—"

He stopped midsentence as he realized where he was. He looked down on Sombra, and he quickly shook his hat off. He was blushing while Sombra didn't even crack a smile. "I'm going to pretend I have no idea what you were doing and just get down to the point: what is that thing headed over here?"

"Is Nightmare visiting?"

"Focus!"

Discord gave him a blank look. "Seriously? You are asking me, a lord of Chaos, to focus on something? It's like you don't know me at all."

"DISCORD!"

The god of Chaos sighed as he conjured a pair of binoculars. He peered out of the window and chuckled. "That's nothing more than a simple weather balloon. Haven't you heard of the Balloon Colt that caught Equestria's eye a few ye—"

Sombra's neutral expression said it all. Discord chuckled. "Ugh, nevermind. It's probably a piece of junk I accidentally conjured up and it left my watch. I'll put it away."

With a snap of his claws, Discord vanquished the box. Immediately after it disappeared, it reappeared in the sky. This caught Discord's attention and he tried snapping his claws again. Again it disappeared and reappeared within a second. He clapped and stomped the ground, trying to vanquish the box, but he had no luck.

He sighed. "This usually works," he said.

Sombra roared in anger. "If you need something done right, do it yourself. Move out of the way!"

Sombra smashed the glass with his hoof and charged up his magic. He fired a beam of dark energy at the box and held it in a tractor beam. He smiled and laughed at Discord for struggling with something so easy. He fixed his attention back onto the box he held onto, but it was gone. Sombra let up his dark magic and stared at the point where the box was last located.

"Umm, what just happened?"

"Well performance issues, it happens a lot. 1 out of 5—"

"Shut up Discord," Sombra said.

The draconiquus chuckled. "Well, it seems as though neither of our magics can hold the box, so I think it's just some sort of illusion. There is no way that anything on this planet can withstand that mag—"

The castle rumbled above their heads. The box was flying up the castle, passing the two rulers. A strange wheezing sound seemed to be emitting from the box itself. Discord had gotten a better look at it. It was a blue tall box with two doors in the front. There was a small light on the top of the box with a sign on it. He didn't catch the sign because it was moving too fast. That wasn't the only thing that caught his attention, however.

As the box passed him, he noticed the wheezing sound as it flew. He had heard that sound before. He dove into his memories and latched onto where he heard that sound before.

_1000 years ago…_

_Discord laughed as he viewed the world below him. He had turned the desert into dessert and the Unicorn Range into the world's largest taco. He had made the clouds rain chocolate milk and volcanoes spew rainbows in the Bad Lands. He laughed as ponies tried running from whatever the hell was going on. He fixed himself a glass of chocolate milk and drank the glass itself. He couldn't stop laughing as one pony yelped before turning into a tree._

_As he looked around his new world, he noticed the Castle of the Two Sisters remained untouched. He wondered why it had survived his chaotic meltdown. He teleported into the castle and transformed into a unicorn guard. As he did so, a guard turned the corner. Discord yelped mid-transformation, but blowing a green dust in the pony's eyes forced him into a quick nap. Once the draconiquus was fully transformed, he hoisted the real guard and hid him behind a statue. He fixed his fake helmet and began to wander the halls._

_It took a few minutes, but he had found the throne room. He leaned his ear against the door to the throne room. Celestia and Luna were arguing about what to do with Discord. Luna wanted to vaporize him, but Celestia thought about trapping him. Both were impossible in the draconiquus' eyes, but he continued listening. Luna appeared to be convincing her sister on what they had to do, and before he made his escape, he heard Celestia gasp._

"_He's here!"_

"_Already? How did he—?"_

"_I do not know, dear sister, but we are ready."_

_Discord froze. He expected the sisters to break the doors down, but he heard something else. A wheezing sound seemed to be emitting from inside the throne room. He continued listening and he noticed that the wheezing was getting louder, like something was approaching. The sound reached its peak before it quickly became silent._

_He heard a wooden door open, which was strange to the disguised Lord of Chaos. Celestia was the first to speak. "My doctor, why have you come?"_

"_I found what you need to defeat Discord. Well, Starswirl and I did. We found this map in a chest on the shore of Equestria. Here, let it guide you to where you need to go," a stallion said._

_There was a short pause, followed by Luna's voice. "We do not understand, this map is hundreds, maybe thousands of years old. How can it be—"_

"_Listen, you have to trust me on this. Follow the map and you will find them. I was never here."_

_Discord heard the wooden doors open and close. The wheezing sound began to grow again, and before Discord could storm in and find the stallion, there was silence. "Sister, can we trust him?"_

"_He has helped us in the past, and I believe in him today. This is a lead on where they are!"_

"_If they are here, then we can win?"_

"_Maybe. Come, we must prepare."_

_Discord took that as his sign to get out. At the time, he thought he was just hearing things. He had no idea the subject in question would turn out to be the Elements of Harmony and he didn't expect his defeat later that afternoon._

Back in the present…

Discord was staring into space. His eyes were twitching as the memory unfolded. Sombra was confused. "Umm, hello?"

The draconiquus turned to Sombra. "I just realized I left the stove on at home. I really do need to go," he lied.

Sombra was confused. Little did they know the TARDIS had materialized with its cloaking shields up. Twilight snuck out and magically tied Sombra's tail with Discord's. She quietly giggled to herself before returning to the control room. She silently closed the doors behind her and ran up to the Doctor.

Rainbow Dash and Zecora were both inside the TARDIS, and their mouths were still hanging. Bigger on the inside seemed impossible, and it wasn't until now that Rainbow realized that Twilight's house at the Golden Oaks library seemed to be bigger on the inside. While she did have a large library, her loft, bathroom, kitchen, and living space made the treehouse seem smaller on the outside. She decided not to think about it too much and tried understanding the concept of an old police box with an inside that could fit all of Ponyville.

The Doctor turned on his monitor and set it to 'Home Theater'. A large screen appeared from behind the Doctor with a live picture of outside the TARDIS.

"You don't understand, I have a rouge blue box flying around that can be trouble. Why are you suddenly scared of it? What, did it destroy your life?!"

Discord gave Sombra a dark look. "You have no idea. Anyway, I need to see Nightmare. I do believe I owe her a reason why I vanished in the middle of a good joke. The box is in the Crystal Empire, so it is your problem. Now, if you excuse me."

Discord vanished. Sombra felt something pulling his tail, and before he had time to think, he vanished too. Everyone inside the TARDIS started laughing as they rewinded Sombra's face as he disappeared. To the Doctor, it reminded him of a cartoon he caught himself watching about a cat and a mouse fighting in a house. Rainbow and Twilight were in tears while Derpy, Luna and Zecora were rolling on the floor.

The Doctor calmed down. "Ok, that should buy us a few minutes. Let's find Rarity."

* * *

><p><strong>AN: I realized that this chapter should've been the TARDIS crew finding Rarity, but having a chapter with Discord and a member of the 4 seemed to be like a better idea. Rescuing Rarity is up next, followed by Applejack and then the dungeons of Canterlot. A little spoiler for you.**

**Somepony knows the Doctor's secret and where it will be told.**

**Until next time. Peace out!**

**-SirScribe**


	15. Rarity

**A/N: Greetings ponies and welcome back to Dark Vengeance! I've been successful in getting **_**Starswirl's Nightmare **_**and **_**New life in Ponyville **_**out without a problem, and with that, I can get back to work on this little beauty. I must say, the support for this story is amazing. I do enjoy writing for all of you, and once I get everything I want to write out of my head, I will branch off with oneshots and solo adventures. I might start one after this story is complete. I am dreading the completion of this story, but it's too fun to write.**

**Pinkie: Fun?**

**Me: Don't you dare**

**Rarity: …**

**Me: What's wrong?**

**Rainbow: Are you still mad?**

**Rarity: A lady does not hold a grudge**

**Rainbow: Thank Celestia**

**Rarity: BUT YOU SLUNG MUD IN MY BOUTIQUE AND TRIED LYING ABOUT IT!**

**Rainbow: *flies in fear***

**Me: …well that was a bit weird. Anyway, I don't own MLP:FiM. All rights belong to somebody else (I'm betting its HASBRO)**

**ONWARDS!**

* * *

><p>Shining Armor felt guilty and distraught. With Sombra's return to the Crystal Empire, he led the front lines against his invading forces. He and his brave soldiers fought hard and through the front lines, and he was close to claiming victory against the Frightful Four (Sombra, Discord, Nightmare, and Chrysalis) before things turned south.<p>

Shining had defeated the first wave of changelings and Shadow Ponies. It appeared as though it was going to be easy to hold them off, but he was sorely mistaken. Before he could rest, however, Rarity stood up and faced him. Feeling like his hooves were glued to the snow and his magic depleted, Shining was quickly overpowered. With his lines shrinking, Cadence's Royal armies began to hold the borders, but Sombra was too powerful. Within a moment, Cadence was beaten.

With the royal couple defeated, Sombra was elated to share the news of Canterlot's fall. "Celestia crumbled like the little filly she is," he said.

"My sister and her friends will stop you!" Shining shouted at the tyrant.

Sombra laughed. "I forgot to mention: Princess Twilight's reign fell as she did. Her wings are clipped and her time has passed. The Elements are dead!"

That threw Cadence into a depression. She saw Twilight as her own sister, and if Sombra was right, she was dead. They both did nothing to fight and were both thrown into the dungeon under the city. With only his wife in the prison, the prince of the Crystal Empire began to sob.

Cadence, on the other hoof, said nothing. She didn't know what to say. Her sister-in-law was dead. With no power to fuel the Crystal Heart, the Empire fell almost overnight, and she had to watch as her subjects lost faith in the monarchy. Sombra opened the mines and forced his subjects into slavery just how he had done before. The ponies who were able to pay Sombra's taxes were spared from slavery, but received harsh responses from their fellow citizens.

As Sombra laughed at the misery of the Crystal Empire, Shining shed some tears as he quietly mourned his sister's death. Cadence picked up a rock and began carving into the wall of her cell. Occasionally, she would slam the rock into the wall, reducing it to dust. Shining looked over at his wife and held her as she picked another rock up. She wasn't angry, she was just too sad.

"What can we do now?" Cadence asked.

Shining looked up at the cell. "Wait until somepony stops Sombra. Somepony has to have the strength to fight him," he said.

"But if Celestia and Twilight fell, then who—"

Cadence looked over at her husband. "Princess Luna!"

Shining nodded. "Maybe she can fight Sombra and free us. At least we need to Crystal Empire to be freed before we have the upper hoof."

Cadence nodded. She knew Luna was tough, despite her recent return to Equestria. Luna was the princess of the Night, and her powers were near infinite. Cadence dropped the rock and lost herself in her husband's embrace. "You know, Shining, there has been something I've wanted to talk to you about."

Shining's heartbeat began speeding up. "Oh, like what?"

"Well, you know we've been married for a year, and our anniversary is coming up in a few weeks, and I was thinking that maybe we should start looking toward the future for us and the kingdom," she said.

"What are you saying?"

Cadence fidgeted. She tried asking Celestia what to say to Shining concerning this sensitive topic, and the wisdom she received was grand.

"_No subtle hints, no stallion is good at understanding hints. Drop it on him if you want him to get it,"_ Celestia said.

"Uh, I was thinking that now would be a good time to introduce a new member of the family to this world," Cadence said.

The gears in Shining's head turned, but nothing was happening. "I don't understand."

Cadence mentally face-hoofed. _So much for that,_ she thought to herself. "Forget it."

Shining smiled. Cadence sighed as she felt her eyelids grew heavy. Before she could drift into a peaceful sleep, a weird sound began emitting from the room. "Shining, what are you doing?"

"I'm not doing anything."

Cadence opened her eyes. The sound was growing louder and appeared to be close. She looked around for the source of the noise, but there was nothing in the room with them. The one guard that was assigned to them was outside the prison doors, but aside from them, there was nothing. The sound was odd. It sounded like something was wheezing like they inhaled smoke or something.

The couple continued searching, but Cadence finally found it. In the middle of the room, a large box began appearing out of thin air. Shining had to rub his eyes to make sure he wasn't seeing things. His eyes were serving him right. A large, blue box was appearing. The box was a panel of windows and a set of large doors on the front. There was a small light bulb attached onto the top of the box. When the box had fully materialized, there was a loud bang. Both Cadence and Shining were stunned.

The doors opened, and a brown earth pony walked out with a long, brown coat. He had a messy mane with a silver stick in it. Cadence wondered how this pony liked going around looking like a crazy homeless stallion. The earth pony looked at the couple and smiled. He turned back to his box. "Yup, this is the right cell. Princess Cadence and Prince Shining Armor right?"

"That is them!" they heard Luna's voice from within.

Cadence lit up. "Luna! Is that you? Where are you?"

Luna stepped out of the box. "Right here. Oh wow Cadence, how is it being trapped in the same cell as your husband?"

Cadence smirked. "Very funny Luna," she toyed.

Luna smiled. "Anyway, we are here to bust you out!"

Shining Armor banged his head on the wall. "Great, I think the guard heard you, if he didn't hear your box first," he said.

Luna realized her mistake and shrunk down in embarrassment. "Whoops."

The stallion shrugged. "Ok, standard bolt door with mechanical tumbler inside the door." He reached for the silver stick. "Setting 46B should do the trick here."

Cadence chuckled. "Excuse me, but that's a stick, it can't open a door. You need a key."

The stallion looked up at the princess. "Hairpins and needles can open locks too. Have faith in my screwdriver."

"You're what?"

Instead of answering, the stallion aimed the silver stick at the door. With a light buzzing sound, the door lock clicked. Cadence was taken back at the magic she had witnessed, and with a simple push on the door, it flew open.

"This is a Sonic Screwdriver. Opens anything, tricks anything, and does everything else, except wood. Maybe some hairdryers too, but I'm getting that fixed. I'm the Doctor by the way," he said as he stretched his hoof at Shining.

Shining shook his hoof. "Nice name. 'The Doctor'! Maybe I should be called 'The Prince'," Shining said.

"Please don't," Cadence said.

Shining smirked at his wife. The Doctor bowed to Cadence. "Nice to formally meet you, Princess Cadence."

Cadence was taken back. Normally she didn't like ponies bowing to her. "Why are you bowing?"

"Luna dared me. C'mon, we gotta get out of here, and quickly. Sombra's guards will be here any minute," the Doctor said.

The royal couple nodded in agreement, and before they could make a move to the box, a magical energy burst hit the door. The four ponies turned to see the guards standing at the doorway. Taking the front line was Rarity herself. She was wearing her crystal military uniform with matching helmet. Her eyes were still glowing green from the dark magic running through her veins. "Trying to escape is not permitted in master Sombra's Empire. You will return to your cells now!" Rarity commanded.

Cadence and Shining held their ground. "You're not defeating us this time, Generous One!" Cadence said. "I don't care if you were Twilight's friend, you are going down!"

Rarity smirked. "I guess you will be seeing Twilight again very soon, dear princess." Without another warning, she fired a blast of dark energy.

Before Cadence could raise up a shield, the doors swung open, deflecting the blast straight back at the unicorn. Rarity dodged it with ease, but the guard behind her did not. The door closed, and out from the box, the princess of Magic stepped out. Cadence and Shining Armor looked shocked and relieved. Twilight was alive!

"That's enough Rarity!" Twilight commanded.

The guards lowered their spears, but Rarity called them off. "It seems as though the new wings actually give you some form of immortality after all. Twilight Sparkle, the first unicorn to successfully control dark magic and its seductive properties. Care for a rematch?"

"Trust me, it won't take long for you to submit. Rarity, please, you need to snap out of it."

"Rarity is dead! I reign supreme, and once my masters fall, all of Equestria will belong to me! Guards, kill them!"

The guards charged at the ponies. Twilight summoned an energy ring from her vast collection of Starswirl's magic spells, and fired several stunning spells at the guards. Most of them fell immediately to the ground while the others continued charging.

The Doctor raised his Sonic Screwdriver, and pointed it at the ground. Immediately the stones began moving up and down like the floor was a waterbed. The guards lost their balance and fell over in full armor. Their helmets knocking them out cold.

Rarity roared as she summoned Shadow Ponies to the room. A legion of 50 raised up and quickly surrounded the ponies and the box. Rarity thought she had trapped Twilight and her friends, but as the walls of the Shadow Pony's magic began to darken, a bright light was seen emitting from within the vortex. The Shadows began shrieking and immediately exploded. Cadence and Shining Armor had created a bright light from their magic, destroying all hopes of more Shadows forming.

Rarity had enough of her minions failing. She fired another spell at Twilight, but she quickly deflected it. The energy flew up into the ceiling, probably spooking a guard off duty. Rarity continued to fire spells at Twilight, but since she read most of Starswirl's notes on advanced combat spells, she was able to break down every single attack and easily deflect them. The attacking unicorn began growing impatient with her adversary and threw 3 quick spells, but not at Twilight.

The princess of Magic followed the magical bolts, and saw where they were going to hit: Cadence, Shining Armor, and the Doctor. She couldn't focus on all three at once with her magic. She fired two magical bolts and intercepted them, and jumped in front of the Doctor, taking the third bolt. It hit her chest, and she immediately went down.

"Twilight!" Cadence exclaimed.

Twilight groaned in pain as she tried to stand on her hooves. Shining helped his sister to her hooves and hugged her for the first time since the mirror trip all those months ago. Rarity grinned as she towered over the injured princess. "Yield!"

Twilight rose to her hooves. "Rarity, please snap out of it. You can do it!"

Rarity laughed. "I fell for that once, but I have learned. No amount of Rarity's magic or your friendship will save her! Yield, or your brother dies!"

Luna flinched at Rarity's foolishness. Rule number 1 of anything is: do not threaten family. Twilight charged up her horn. "That's one."

Rarity was confused for a second, but she fired a magic blast at the princess of magic. "Two."

Another magic blast hit the princess. "I said yield!"

Twilight looked up at Rarity, and smiled. "Three."

Immediately, Twilight took the offensive. She fired magic spells left and right, sending Rarity back. The unicorn felt all the power from Twilight, and the darkness inside was actually scared out of her mind. Twilight continued her barrage of stunning spells, attacking the physical Rarity. While a part of her tried to hold back her attacks. It would take a lot of power to force the darkness out of her completely. Besides, with the walls between Rarity and the darkness thinning, the chances of Rarity being freed were skyrocketing.

Rarity stumbled as the last magical blast hit her. Her eyes were shifting from green to blue, but the green was winning back control. Twilight knew this would happen, and with Rarity struggling to the surface, the next step of her plan was being put into effect.

Rarity fell. The darkness within her was fighting to keep control, but Rarity was fighting back. Twilight smiled. "Ok, now it's time to give me my friend back!"

At that moment, Rainbow Dash flew out of the box and stamped a necklace onto Rarity. At first, she shrieked at the sudden intrusion, but shrugged it off after realizing she put on a piece of jewelry. It was a gold necklace with an array of emeralds as the pendants. "Did you really think that a simple necklace will stop me?"

Twilight shook her head. "No, but that's because it isn't just a necklace." She fired a magical blast at the necklace, and it transformed. The emeralds all morphed into one single gem, and with a slight color change, the gem turned red. Both Rarity's recognized it immediately: it was the Fire Ruby.

Rarity was in shock. "Rarity, I know you can hear me right now, and you need to know this. We need your help. We all do, and we want you to just come back home. Please, Rarity, come home."

Tears began to form. "Ho-home?"

Rarity's horn exploded with magical energy. Twilight and the rest of the crew shielded themselves from the blast. "Twilight!"

The alicorn looked into the epicenter of the blast. There was Rarity with two heads. One had a face of concern while the other had anger.

"Twilight, help me!"

"NO!"

The two Rarity's faced eachother. The dark magic Rarity swung her hood, nailing Rarity in the muzzle. Rarity tried to fight back, but Twilight knew she couldn't. "Return to me!"

"Rarity, you have to fight it!"

"I can't!"

"Rarity, think about all the ponies who need your help! Think of Spike! He's under Nightmare's control, and if we don't stop them fast, who knows what will happen to him. Who knows what will happen to all of us. Please Rarity, you're stronger than this," Twilight said.

The dark Rarity raised her hoof and brought it down. Before it could land on her, a magical hold was placed on her hoof. "That. Is. ENOUGH!"

Rarity threw her own hoof away and fired a beam of magic into the muzzle of her dark counterpart. The dark Rarity screamed as her form cracked. "I am one of many! YOU CAN'T STOP ME!"

The dark Rarity's form shattered into billions of pieces. The magical field dimmed as the winds died down. Rarity's eyes rolled up into her head as she slumped down. Luckily, Rainbow Dash was there to catch her. Twilight sighed as at least one of her friends was saved.

She turned to the Doctor. "Will she be alright?" she asked.

The Doctor came over to her and performed a quick inspection. "Yes, she will just rest. Your attacks were focused on the dark force within, absorbing all of the hits. You never struck Rarity down at all, but I think we should avoid doing the same to your other friend, Applejack right?"

Twilight nodded. "Ok, Rainbow, help Twilight bring her in. Shining Armor, Cadence, I can drop you both off at the borders of the Empire. I've had a small army amassed there for you to take back the city. If you manage to drive Sombra out, wait until the right time to activate the Crystal Heart."

Shining nodded. "Ok, two friends down, 3 more to go. Oh boy. Ditzy, I may need an extra cuppa tea before we hit the Vortex!"

"Gotcha!" Ditzy called from within the TARDIS.

"Now little pegasus, don't be shy, add the sugar and reach for the sky," Zecora said from within.

"Why am I doing this?"

"The cups of tea are above, and I do not have the wings of a dove. You will reach and I will watch, as the tea is prepared with scones in a batch."

The Doctor was going to have a headache with Zecora before they finish their quest.

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><p><strong>AN: Ok everypony, that is it for now. Another chapter will be up as soon as possible. School is starting back up later this month, and I need to get my head in the game. I've decided that my next MLP/Doctor Who series will be taking place on the official MLP fanfiction website, fimfiction. Once this is done, expect the first chapter of the next season of Doctor Whooves' newest adventures. Until next time.**

**-SirScribe**


	16. Applejack

**A/N: Greetings everyone, and welcome to **_**Dark Vengeance!**_** I am so sorry for being absent over the past month and a half I believe. I've been working one some new fics, and if you haven't already found them, you can always search **_**Whooves N' Jack: Time-traveling Foal Sitters. **_**It's not on this site, however. After this, and once my other stories on here are complete, I will be fully into creating Whooves N' Jack a reality. Remember, you can follow me on Twitter sir_scribe for updates on the story.**

**I owe you guys a lot, so I will be putting out two chapters of **_**Dark Vengeance **_**and 1 more chapter of **_**Starswirl's Nightmare.**_** That chapter may be the last update for that story. As for **_**New Life in Ponyville, **_**I don't know. Leave a review on whether or not I should continue that, as well as your thoughts on the chapters coming up.**

**Twilight: Too hot! Princess Celestia is mad today!**

**Me: Tabloids?**

**Twilight: Worse!**

**Me: Bad cake?**

**Twilight: WORSE!**

**Me:…um, I give up**

**Twilight: Somepony started putting up posters that proclaim that she has a plot as big as the Moon, and the heat wave won't cease until she finds who did it**

**Me: …**

**Twilight: Anyway, SirScribe doesn't own MLP:FiM. All rights go to Lauren Faust and Hasbro Animation Studios. **

**Me: Well then, on with the show?**

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><p>Applejack gave one last good buck before the tree came down.<p>

With the taste of the apple treat she had to endure while masquerading as Princess Cadence, Queen Chrysalis ordered that many of Equestria's apple orchards had to come down for good. Any pony who had great strength were 'hired' to bring them down. In return, she would not bring harm to them. If that didn't work, then classic hypnotism worked best. Still, Chrysalis kept her word and brought misery to those who resisted.

Applejack was working in the orchards of Appleloosa bringing down the trees. Because of her experience and strength, she was best qualified for the demolition. She and a few other ponies worked together to bring them down, and high in the gorge surrounding the orchard, were the Changelings watching their workers bake in the eternal darkness that Nightmare created.

As the tree finally rested on the ground, Applejack breathed a big sigh of relief and felt pleasure. Her sickly green eyes glowed with the power the Changelings used on her. She surveyed her work in front of her. So many of the apples were smashed under the weight of the now dead tree. As she surveyed her work, she noticed a simple red apple on the ground, completely unharmed. No sign of bruising or anything.

Applejack walked over to the perfect apple, and smashed it with her hoof. She had her orders. No apple gets any mercy.

As the apple farmer turned to tackle her next tree, she found herself face first into a pair of wooden doors. She hit the doors with such strength, it wiggled. She bounced right off and landed on the ground. Her Stetson flew into the air and landed nearby…next to another perfectly fine apple.

Applejack groaned as she looked up at what hit her. It was a big, blue box. That was it. A simple blue box with window panels and a pair of doors. Above the doors and window panels was a black bar with the words: POLICE PUBLIC CALL BOX. At the very top was a simple light bulb.

"Well that can't be right," Applejack said to herself. "That wasn't there a minute ago."

Boy was she right. She walked around the box, looking for whoever put it there in the first place. She knocked on it in several places. It was 100% wood. It also looked pretty heavy. Applejack did another walk around just to ensure she didn't miss anything. Aside from the handles, there was nothing else abnormal about it.

The pony reached for the handles to see if the box can open, and before she could push the doors open, they flew open. Applejack jumped a few feet back as a brown pony walked out. He had a messy brown mane and wore a long, brown coat. Sticking out of the pocket of his coat was a silver stick with a blue tip. She thought the stallion looked weird wearing something so…outstanding. And not in the best way too.

The stallion closed the doors behind him. Applejack could swear she saw something inside. Before she could say anything, the stallion spoke. "Hello Applejack," the pony said.

Applejack raised an eyebrow. "Who are ya?"

"I'm the Doctor."

"Doctor what?"

The stallion chuckled. "Just 'The Doctor'. Nice to meet you," he said.

Applejack sighed. "What do ya want? No, don't answer. Leave!"

The Doctor sighed. The Changelings had a lot of control over the farm pony. He had managed to convince Twilight that he was going to snap Applejack out of her hypnotic state. The Time Lord took a step toward her, but Applejack took a step back. "Don't come any closer! Ah'm warning ya!"

The Doctor stopped. "Why don't ah just spare y'all the trouble and git! Why don't ya leave like the rest of 'em!"

"This caught the Doctor's attention. "Like who

"Like Twilight."

Inside the TARDIS, Twilight was overhearing everything. When Applejack used her name, the princess of magic felt like she was frozen. Rarity, who had recovered from her earlier fiasco, was also overhearing the conversation.

Rarity had completely recovered from being Sombra's puppet. The armor she was forced to wear was now gone and the effects of dark magic was completely wiped out. It was as though nothing happened to her, but she knew very well that Sombra used her the way no pony should ever be used. It made her feel dirty to take an empire for the wrong cause.

"Why did she say your name, Twilight?" Rarity asked.

"I don't know. I didn't leave her or anypony like I abandoned them," she said. "I stayed as close as I could."

Ditzy and Luna both looked at each other. "Perhaps this is not for us to be involved in, wouldn't you agree?" Luna asked.

Ditzy nodded. Together, the two friends left the control room in search for something to pass their time. Zecora had been dropped back off to Ponyville after recovering Rarity for, what Twilight called, the right moment to strike. Zecora didn't know what to think of that in the beginning, it made perfect sense that Twilight wanted her to help organize a rebellion against the Four.

The Doctor sighed. "Why would Twilight be involved in this? She would never leave you."

"Yeah she would! She's a princess now! A fancy pony with wings and a horn! She's practically a god now, and why would she want to hang around us when she could be with the princesses performin' their royal duties in elegance? We ain't nuthin to her!"

The Doctor immediately walked forward, this time with no resistance from the hypnotized pony. "Well, don't say that. Yeah she is an alicorn now, but that doesn't mean that she—"

"She's immortal, aint she?"

The Time Lord took a minute to think about the question. "Twilight will probably live her life with us, and when we die, she'll forget about us! Ah though we were going to be friends forever, but that can't happen if Twilight is living for thousands of years! First mah parents die, now my friendship with Twilight will die. Ah'll never get to see Twilight like she'll see me. Ah'm going to be old and a granny while Twilight will look the same as now. Ya don't understand what it feels like to know your friends will forget about you and you can't do anything about it."

Twilight froze inside the TARDIS. Rarity was also frozen when she heard that Applejack was telling the Doctor what she was thinking in the past few months. She did fear that Twilight would outlive her, and she had talked to the others who all shared the same fear.

The Doctor sighed. "Well, don't assume that," he said.

Applejack looked up at the stallion. "You think she will forget you when she hits the millennia mark? That's impossible, Applejack. I'm 904 years old and I remember all the faces I've met over the years."

The Doctor's expression darkened. "All the faces I lost. All those ponies didn't deserve to be put in harm's way."

Applejack sat up. "Yer not 904 years old. Ya ain't an alicorn!"

The Doctor shrugged. "Well, that depends on the race. Listen, I cannot say for sure whether or not Twilight is immortal, but that doesn't mean you should abandon your friendship with her over the possibility that she might be."

Twilight's heart raced. "I've seen a lot of things in my 900 years of time travel. I've met spectacular people and ponies within that time. I grew attached to each friend I made, but I had to accept the ugly truth at some point: it won't last forever. You think it will last forever, the friendships, but they don't. They wither and die just like everypony else, but that's in the eyes of immortals. Immortals will see the birth and death of whoever they come across. They can't fall in love because it is temporary. They can't have a family when only one or two of your foals will regenerate.

I've lost so many of my friends, they all are blurred now. Their lives are racing away, tackling new obstacles and combatting old sins. They're also living. They find love, they have foals, and their foals will later have little ones. It's an adventure to see where life takes you, but if you are frozen in time, like myself, it's nothing more than looking into the window of a shop and imagining yourself with the item, but you can never have it. It's cruel."

Twilight's heart broke. "If Twilight is immortal, then you got the better end of the deal. She can live her life for a long time and can probably do a lot with her free time, but you, no. You can work as much as you can, settle down and find somepony to share your life with, have a family started, and overall enjoy life. You can do whatever your heart desires and it will be enjoyable. That's the meaning of life. We don't try to avoid death because we fear it, we avoid it because there is still much to do. What's life without end?"

Applejack sniffled. "Don't think Twilight will forget you. You made a lasting impression on her, you all did. How can somepony forget who her extended family is? You all will hold a special place in her heart. Don't let time boss you around."

Twilight moved herself from the door, allowing Rarity to continue listening. She was going to have a talk with Princess Celestia when this was all done. While Rarity stood by the door, her mind began to race. The Doctor was letting on more than what he already shared. 904 years old?

Applejack's eyes began to water. The green glow that symbolized the hold the Changelings had disappeared, giving her free will. She ran to the Doctor, and gave him a big hug. The Doctor smiled as he returned the hug. The first thing Applejack heard was a series of drumbeats. They seemed to be coming from inside his chest, where his heart was supposed to be. Even though it was troublesome to hear the foreign sound, it was relaxing. Listening to a heartbeat was soothing as it was, but this drumbeat was something else.

The two broke the hug. "I think you are all well. C'mon, we should continue looking for your friends."

Applejack nodded. "Um, did ya say that Twilight is alright?"

The Doctor nodded. "Um, can ya not tell 'er about this?"

"Keeping secrets is my specialty," the Doctor said. "Ok, so you, Rarity, Rainbow Dash, and Twilight are all secure. Now, I understand there are more."

Applejack nodded. "Ah think ah know where they are. Do ya know how to get there?"

The Time Lord smiled as he knocked on the doors of the TARDIS. Rarity took that as a sign to get out of the way. The Doctor threw open the doors. "Care to step inside?"

The earth pony looked inside, and already her mind exploded. The console room was inhabited by Rainbow Dash and Rarity, who were both talking. When they saw Applejack, they both dropped whatever else they were doing and reunited. Applejack's heart began to fly as she embraced her friends once again. As they united, the Doctor looked around for Twilight. He knew talking to her about the whole situation with immortality would be a sore issue. The Doctor returned to the console and released the brakes of the TARDIS.

"Ok Applejack, I'm going to need your best guess. We got ourselves ponies to round up."

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><p><strong>AN: Well peoples, I hope you liked this chapter. The next chapter should be up right after this, followed by what I think should be the finale of **_**Starswirl's Nightmare**_**. **_**New life in Ponyville**_**, however, remains unknown. If you read that story and want to see it continued, please let me know. If not, I will post the finale very soon. Again, thank you for your time and patience. **_**Whooves N' Jack: Time traveling Foal Sitters**_** is already out. Until later**

**-SirScribe**


	17. Fluttershy, Celestia, and Pinkamena

**A/N: Greetings ponies and humans of the world, SirScribe here with another installment of **_**Dark Vengeance**_**. Thank you for your patience and support for this story, I think it's my favorite fan fiction to write. I hope you all are enjoying the school year (yeah right). School is back on for me and this time, it isn't so bad. I have a flexible schedule of school and work, both labor and fiction. I'm working with someone on creating a new story, but it isn't going to touch MLP, I think. With MLP in mind, I'm getting started once again.**

**Reminder: There will be no more new stories on this account once all the present stories are complete. Everything else will be on m account. Once the **_**Whooves N' Jack**_** saga ends, I'll begin working on other works, leading up to my series finale: **_**Equestria Girls: Armageddon.**_

**Celestia: Armageddon?**

**Me: Yeah, why do you sound surprised?**

**Celestia: I'm not surprised.**

**Me: Oh. Princess Celestia of Everfree everybody. She was here for **_**Starswirl's Nightmare**_** recently, and before she returned to her royal duties, I felt it would be nice to have her back in the studio.**

**Celestia: Oh yes, we are preparing for a major celebration in the coming months. Nightmare Night is coming up, followed by Thanksgiving, and then Heart's Warming so we have to be ready for all those holidays**

**Me: Thanksgiving? Minus the turkey, right?**

**Celestia: …**

**Me: Never mind. Anyway, would you care to do the honors?**

**Celestia: Certainly. SirScribe doesn't own MLP:FiM. All rights go to Lauren Faust and Hasbro Animation Studios.**

**ONWARDS!**

* * *

><p>Fluttershy was bored. So, so bored.<p>

Shortly after she, Pinkie Pie, and Princess Celestia were thrown into the dungeon, Fluttershy developed a need to talk to somepony. Her blindness, a result from Nightmare Moon's magic, left her with a desire to talk. Of course, Pinkie fell silent right away while Celestia was slipping in and out of consciousness. With the guards all the way upstairs and no other forms of life downstairs, Fluttershy found herself talking to the wall.

After a while longer, she too became silent. Occasionally, Celestia would awake and speak to the pegasus. It made them both happy. Fluttershy would talk about how her animal friends would sometimes chase Rainbow Dash around, especially the flying creatures she denied having as a pet. Celestia laughed and explained how she came across her Phoenix. Eventually, however, Fluttershy returned to the silence she had grown accustomed to. She began to bat at her own tail and occasionally hum some tunes her songbirds played. Some of the tunes were familiar to the princess, and they hummed a duet.

Then Fluttershy ran out of songs to hum.

As Fluttershy stayed silent inside her cell, Princess Celestia contemplated her situation. Her horn was broken and her Magical Core was exposed. She should've gotten out easily, but thanks to Nightmare and Chrysalis, the guards believed they have detained criminals who attempted a coup. Celestia began to wonder if Twilight was still alive. The Elements are the only thing that could save them from this awful nightmare. If Twilight didn't survive, then hope is lost.

The more she thought about the Elements, however, the more she began to wonder where they came from. The first time she saw them was after the Doctor and Starswirl told them where to find them. Upon arriving to the Tree, however, Celestia felt like she had seen them before. Thinking about them now, Celestia knew that she would have to search for the answer to the question: when did I first see the Elements?

Her concentration was interrupted by the sound of a wheezing machine. Celestia's ears perked up. It couldn't be—

Celestia rose from the floor of her cell, cautiously while doing so. Indeed, the magical blue box was starting to materialize in front of her. Next to her, Celestia thought she heard Fluttershy squeak in fear as the sound grew louder. Celestia smiled. She first heard the sound…well, it was a long time ago.

The blue box finally took a solid form. Celestia's heart began to race. The doors of the wooden box opened, and bathed in a white light, the stallion emerged. He was brown, unlike the last time she saw him. His ship also looked different. New or old TARDIS, she could never tell the difference.

The stallion ran over to Celestia's cell. "Princess Celestia!"

"Doctor! Oh mother of Me, it's good to see you again," she exclaimed. "New regeneration?"

The Doctor looked down at his body. "No, I've been this way for about 300 years now. Jumping from place to place though, never staying in one time. It gets boring."

"At least you get to cheat. I have to progress the long way around," Celestia said.

The Doctor chuckled and reached into his pocket. He pulled out his Screwdriver and began working. "Coast is clear, come on!"

Celestia looked up, more ponies were walking out. Applejack and Rainbow were both the first to exit. Rarity followed suit with the gray pegasus behind her. Celestia remembered her as the mare who almost caused the recent Summer Sun Celebration to go out of control. Although it was never proven that it was Ditzy who released the bulls from their pens.

At least, Princess Luna exited with a familiar lavender alicorn behind her. Celestia's eyes watered. Her student was one tough cookie to crumble.

_Cookies sound good right now,_ Celestia thought to herself.

The sound of a turning lock drove her out of her thought. The cell door came open. Celestia was able to slowly crawl out of the cell before losing her stability. Luckily, the Doctor was nearby and caught her before she hit the ground. Her broken horn was still affecting her. The pressure was starting to become unbearable.

The Doctor looked up at her horn. "Hmm, basic fracture, magical leaks are starting to arise along with, it appears to be added pressure. Magical Core is exposed so you cannot meet any enemies on the battlefield until you are properly healed," he said.

Celestia nodded. "Ok, Luna, help your sister to the infirmary. Make sure she is given 'Time Dose 15' with a little bit of Basic Regeneration. Not too much."

Luna nodded and took her sister. Together, they walked into the TARDIS. Meanwhile, Twilight and Rarity were both trying to break the magical seal over Fluttershy's cell. It appears as though Sombra had taken precautions in locking up members of the Elements. The seal itself was already weakening as the Doctor raised his Screwdriver up.

The field began to grow visible. The field was beginning to falter as the three continued to fire their 'magic' at it. Finally, the field fell, leaving the cell wide open. Fluttershy, still blinded, began feeling her way out of the cell. Finally, she bumped into Rarity and Twilight. The girls all hugged each other, and soon Applejack and RD followed.

The Doctor and Ditzy smiled. _5 down, one to go_.

After a while, the 5 began to settle down. "Ok, all we need now is to find Pinkie."

"She should be here. I heard her a while ago," Fluttershy said.

The girls all looked around the prison. The Doctor began to inspect one of the cells when he heard scratching on the cell walls. He followed the sound to a cell shrouded by darkness. Without magic, the Doctor knew there was a powerful force surrounding the cell.

The sound of Pinkie's giggling filled the prison, but it didn't make anyone else feel happy. In fact, there was fear in the room. The Doctor was sure this was the right cell. He placed a hoof onto the cell door, and a face slammed itself onto the bars. It was Pinkie Pie, somewhat.

Aside from her usually fluffy, but now flat mane, the wicked smile, and the bulging eyes that stared into your soul, nothing was different from the earth pony baker. Twilight was alarmed and she came over to Pinkie's cell. "Pinkie? Are you OK?"

Pinkie turned her attention from the Doctor to the princess for a moment. "Why wouldn't I be? I mean, afterall, I was the last to be rescued."

The alarm began to blare in Twilight's mind. "We didn't know where you were."

Pinkie giggled. "Oh, and stop calling me Pinkie. Sounds childish."

"Then what can I call you?"

"Pinkamena is fine. My real name is Pinkamena Diane Pie, but nopony ever really asked for it. As for you, Doctor."

She turned again to the Time Lord. "Names are powerful. They define you. Why is your name shrouded in time? Why is your name the most dangerous word in the Universe? Why do you call yourself 'Doctor'? Doctor who?"

The Doctor came closer. "The Doctor has a name, and it is a secret he will take to the grave. Coming soon to a Universe near us, the question will be answered."

The hairs on the Doctor's neck rose up. "The Doctor's here! The Doctor's here! And death will follow! The Dark Lord has come!"

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><p><strong>AN: Ok, Pinkie lost her mind. The Dark Lord has come, but will he rise like before? Tune in next time to **_**DARK VENGEANCE!**_** Leave your reviews and I will return as soon as I can. **_**Starswirl's Nightmare **_**i****s ending soon. Until next time, Keep Calm and Flutter On**

**-SirScribe**


	18. The Doctor confesses

**A/N: Greetings everypony and welcome back to **_**Dark Vengeance**_**. Thank you so much for the support of this story, it really means a lot. I've been brainstorming a lot lately, mainly for MLP stories and how to make them work. I want my stories to be completely different from what others have written. **_**Dark Vengeance**_** is an example. It is fun to write, plus its part of my headcanon. This profile was also supposed to help predict what was in the Chest of Harmony, and after the finale, I was both relieved and disappointed. I thought there was something physical in there. Oh well.**

**Just Call Me J, thank you for following the story up to this chapter, and hopefully future ones. You are a great support for this story. Yourself, Cool Cuttz, and Dark Sault are all awesome for being so involved in this story. And to all of you who are taking the time to read this, thank you. That's something every author has the privilege to say.**

**RD: Don't start getting teary-eyed**

**Me: Sorry. Rainbow Dash joining us from the Season 5 premier everypony. So, Rainbow Dash, any spoilers for the viewers?**

**RD: It's worth the wait. We had to delay because Discord accidentally rewrote half of the season, so we had to go back and fix it. Fluttershy is keeping him on watch, though.**

**Me: Just the wait?**

**RD: It'll be cool. The whole season will be awesome. We also have a few new ponies walking about, and a plot twist in a future episode. I'm not saying more**

**Twilight: You better not. Great, now we have to go back and edit some more scenes. Thanks, I think you extended the time for the premier.**

**RD: Whoops**

**Me: Well, there's that. Anyway, let's get this party started. I don't own MLP:FiM. All rights go to Lauren Faust and Hasbro studios **

**Twilight: Where's the prop master?**

**RD: Went home, said he was sick. **

**Twilight: We're never getting episode 20 done!**

**Onwards?**

* * *

><p>Ditzy looked at the pink baker in the cell. Pinkie was dancing in her cell, repeating her last words. "The Dark Lord has come! The Dark Lord has come!"<p>

Twilight looked over at the Doctor. He was nervous. The brave stallion who could run head on into an army was gone. All that was left was a coward. She was going to interrogate him later, at least without Pinkie in the same room.

Sorry, Pinkamena. The earth pony stopped her dancing and finally stood still. "Oh, and it looks like he has it all here. The TARDIS, the Sonic Screwdriver, the companion who doesn't know that the stallion she has been traveling with is really a mass murderer who shouldn't be alive, and the regret on his face. What's wrong Doctor, am I upsetting you?"

The Doctor snapped out of his trance. "As a matter of fact, no. I'm just surprised you heard of me. I try to stay out of the history books."

"I didn't recognize you from the history books, dear Doctor. Lord Doctor of Gallifrey is all alone now. So without a companion he once knew as a friend. So long ago, your friend turned against you. How sad of a day that was for you. Childhood friends turned enemies."

The Doctor's ears perked up. "Excuse me?"

Pinkamena waved off her remark. "Oh well, what has been lost will be found. Anyway, I am curious about a few things. One of them is how the war actually ended. I'm seeing various stories on how it ended, but one can never know for sure unless one asks the sole survivor. Well Doctor?"

The ponies in the room, minus Fluttershy, looked at the Doctor. "Any day now, Doctor. Somepony upstairs probably heard the TARDIS materialize and probably sending for a head of command. You don't have the time to stall anymore."

Silence from the Time Lord. "SPEAK NOW DOCTOR!"

The Doctor growled. "OK! I DESTROYED GALLIFREY!"

All the ponies in the room gasped. Pinkamena smiled as the Doctor came undone. "Please elaborate."

The Doctor sighed. "It was after the fall of Arcadia, Gallifrey's Second City. I was in the front lines trying to drive back the Daleks. I found and destroyed a legion of Daleks, and that was when I had enough. The war was going to burn the Universe if I didn't stop it. The Daleks were coming in by the billions every day. There was no way to stop them by fighting. The Time Lords had an arsenal of weapons locked away, and out of all of them, only one could stop the war. I had no choice."

Twilight walked forward. "So instead of figuring a way out of the war, you destroyed two civilizations and survived?!"

"I had no choice! There wasn't a way out. Either I let the Universe burn or destroy my own people. It had to end with my people, because they were about to destroy Creation if I didn't stop them! I fought two demons!"

"And probably innocent fillies while you were at it!"

"I COULDN'T SAVE THEM!"

Twilight took a defensive stance. "I had no choice. I couldn't save everypony. I had only one way out, and that was burn them. I burned my whole planet and its attackers! I wasn't supposed to survive, but I did! I didn't want to! If you had to make a difficult choice, and both seemed extreme, which would you take?!"

The ponies stayed silent. "I would choose the lesser of two evils."

"Which is what I did! If it wasn't for me, then Creation would not exist anymore. You all would be dead!"

The Doctor turned to the pink pony. "How did you know?! TELL ME!"

Pinkamena giggled. "I see your past, Doctor. So many faces, so many lives. 904 years of running, and now it is time to stop. Your time is up, dear Doctor."

"No, I won't. These ponies need my help, and if I die trying, then so be it! I will not give up!"

Pinkamena smiled. "Don't worry, you won't sleep yet. You have one more destination to make, but it will be years before you get there."

"Where?"

Pinkamena leaned in closer. "You will know when you get the call. The whole Universe will know."

Pinkamena started to laugh. Fluttershy cowered as her friend lost more of her mind. "The Doctor will die once more, when he reaches Trenzalore!"

Pinkamena's eyes rolled into her head as she collapsed onto the ground. All the ponies in the room gasped. Twilight moved the Time Lord out of the way and used her magic to open the door. It was safe to say that Pinkie was alright.

_Granted she still isn't insane._ She turned to the Time Lord, who was quietly entering his TARDIS without a word. Ditzy stayed in the dungeon instead of following the Time Lord. She helped Twilight lift Pinkie from her cell and inside the TARDIS. The other ponies followed close behind. When the last pony was inside, the doors closed and locked.

* * *

><p>The Doctor sat quietly inside his study.<p>

The Doctor didn't just hang around inside the console room like everypony believed he would. Whenever he wanted some quiet time, he would allow the TARDIS to drift endlessly in space, lock himself in his study, and read. He didn't care what he read during his time, all that matter was he had something to keep his mind grounded. In his hooves was a Daring Do book that he picked up during his time as Time Turner in Ponyville. Twilight never guessed that she checked out a book to a Time Lord.

As time went on, he went from reading an innocent Daring Do book to reading the History of the Time War, a book he kept in the library. He didn't like reading through it, but at least he could recall and later surrender to the fact he committed genocide. He was adding salt to the wound willingly.

A knock came at the door. The Doctor looked up from his book. _Who knows where my study is?_

He rose to his hooves and opened the door. In the hallway was Applejack with her hat on the side. The Time Lord sighed but put on a fake smile to greet the earth pony. "Hello Applejack, what brings you here?"

The pony shrugged. "Ah just came out of the orchard, which was huge, and ah just thought ah could get some quiet time since RD was jumping in the swimming pool next door. Ah saw ya leaving, and ah thought that maybe ah can join you, if that ain't too much trouble."

The Doctor raised an eyebrow. "That was rehearsed."

Applejack sighed. "Ok, ah wanted to check up on you. Ya took us out of that dungeon and just left without another word. Ah want to see how you are doing, and apologize for Pinkie's behavior."

The Doctor shook his head. "It wasn't your fault, and it definitely isn't Pinkie's fault. That level of intelligence of the Time War doesn't exist in this Universe. She probably overheard something Princess Celestia said. It is natural and I probably should've expected that. Besides, I'm fine," he said.

Applejack narrowed her eyes. "You're lying."

The Doctor laughed. "That's me, the silver-tongued Time Lord. If you want to come in, you can. I'm not stopping you."

The earth pony nodded and entered the study. Her jaw hung when she saw all the stuff inside. There were dusty old books, walking canes, a large brown hat with a multicolored scarf, and a weird long piece of metal on a desk. At the end of the metal rod was a round, black piece. Aside from the rod, it felt like she was visiting old family members.

Applejack inspected the metal rod on the desk. Inside the round piece of the rod was glass. "That's a Dalek eye."

She immediately jumped back. "Don't worry, it was an add-on. It's officially a Dalek's eye stalk. Inside a Dalek is a creature. The creature needs to see the outside world, so they use an eye stalk to see. It's also a Dalek's weakest point."

"Why do ya have it?"

The Doctor sighed. "A souvenir from a very long day back in my Universe. The planet I used to protect was stolen by the Daleks, so I and my companions flew off to retrieve it, but the Daleks were destroyed before we escaped. This was all I had from that day," he said.

Applejack looked back at the eye stalk. "Umm, Doctor?"

The Time Lord looked over. "Can ya tell me what yer planet was like?"

The Doctor smiled. "I can't just tell you, I don't want to leave everypony else out of it."

Applejack smiled and turned to the door. "Girls, he said yes!"

All the conscious ponies walked into the study. The Doctor facehoofed as they all sat around him. Celestia, who had gotten her treatment and was currently healing, was also in the room. Pinkie was still knocked out, but she wasn't going to miss it, especially since she probably already knows about it. Luna sat next to her sister like she was a filly.

The Doctor turned to Applejack, and laughed. He was speechless as they all sat around the centuries-old stallion. Finally he smiled and he sat down. "Well, Gallifrey was once the crown jewel of the Universe. According to legend, Gallifrey was one of the first to emerge from the chaos of the creation of the Universe. The skies were blazing red and the trees were glistening with silver. Oh it was beautiful. When the Sun sets on Gallifrey, and you had a perfect view of them, the trees would burst into flames.

From beyond the fields of Solace and Solitude, there was the crown jewel: the Citadel. A city that house the High Council of Time Lords. A beautiful city with so many wise ponies. It was beautiful. That was just one city, but there were more. We were once the race the whole Universe looked up to. I remember when—"

As the Doctor went on describing Gallifrey, all of the ponies closed their eyes and imagined what once was a beautiful planet. Everypony knew that once they go to sleep, Gallifrey would rise. Little did the Doctor know, that while he was telling the stories of the planet, his TARDIS had an extra passenger. At the doorway of his study, a sandy-colored wolf stayed. Its eyes glowed as the Doctor relived his younger years. The wolf glowed once more before vanishing, leaving the Time Lord to his memories.

Nopony noticed the wolf was ever there, not even the TARDIS itself.

* * *

><p><strong>AN: Ok peoples, I hope you enjoyed this little chapter. Be sure to review, favorite, and follow for future updates. It is almost over actually. I can get a few more chapters in sometime soon. I will return to **_**Whooves N Jack**_** once all stories on this site are done in case you are following that. Remember to also follow me on Twitter. My handle is sir_scribe. Alrighty then, see you later. Allons-y!**


	19. Taking Canterlot: part 1

**A/N: Greetings whovians, bronies, or both. Welcome back to **_**Dark Vengeance**_**! I hope you all are having an amazing time with your daily lives. I've been reviewing some of the story recently, and I feel, as the creator, I should've done a better job in writing it. By reading the reviews, however, there doesn't seem to be anything to change, mind a few spelling errors and what not. Those can always be fixed in due time. Anyway, I am pumping with new ideas for **_**Whooves N Jack**_**, and maybe even move this story to f.i.m.f.i.c.t.i.o.n. so more can read it. **_**Whooves N Jack **_**takes place after this story, though. I have that problem in making the sequel before I finish making the original. Oh well, it's there and I hope you guys are liking it.**

**UPDATE: Equestria Girls 2 may derail my upcoming story: **_**Equestria Girls: Armageddon**_** by only a little bit. After I make some changes to fit into canon, I will begin writing it. Maybe. I gotta finish **_**Whooves N Jack**_** first.**

**There will also be oneshots available both here and on my other account. Yes, I will try to keep this account active. Some oneshots may either be exclusive here or on f.i.m.f.i.c.t.i.o.n., depending on what happens. Anyway, let's get this show on the road!**

**Trixie: Trixie has a knack of taking shows on the road**

**Me: I figured that**

**Trixie: While Trixie feels the need to hoofslap you, Trixie cannot imagine how much of…er you Trixie will have to clean from her hoof.**

**Me: I'll clean your hoof with something. Anyway, it is time to progress onto the story. I feel we have waited long enough. This is coming close to the finale of **_**Dark Vengeance**_**. Be ready!**

**Trixie: Indeed. SirScribe doesn't own MLP:FiM. All rights go to Hasbro and Lauren Faust.**

**ONWARDS!**

* * *

><p>Cadence and her husband, Shining Armor waited outside the Crystal Empire.<p>

Thanks to the Doctor, many of Shining's royal guards were found and unhypnotised. With more than enough to take back the Empire, the prince waited for his wife to finish the conversation she was having with the Time Lord. Thanks to a spell in his library, the Doctor had given the royal family the right spell to send messages via magical links. This made it easier minus the baby dragon who used to send letters to Celestia from the 6.

Cadence sighed as she reviewed the Doctor's plan. "Are you sure about this? We have found the Heart, and it may not be possible to restore it," Cadence said.

"King Sombra only has a hold as long as he is in the Empire. Right now, he isn't. If you can get to the Crystal Heart and cast a spell on it, you should prevent it from being cursed in the event he tries to return. Just keep it within your magical hold until I give the word. When that happens, activate it," the Doctor said.

Cadence sighed. "Very well. How are my sister-in-law's friends? Have they all been recovered?"

"Yes, and they are eager to get some payback for Sombra's little stunt. Believe me, Canterlot is falling tonight."

The Princess of Love smiled. "Fantastic. We will be waiting for your cue."

"Good."

* * *

><p>Sombra untwisted his tail and sighed as Discord laughed his snake-like butt off. He had dragged the king of shadows halfway across Equestria without realizing it, then took the longest route possible just to bring him back to Canterlot. Chrysalis also tried suppressing her laughter while Sombra cursed the god of Chaos.<p>

"Through the Unicorn Range, Discord? You had to drag me through that damn range?!" Sombra boomed.

"I'm trying to have some fun here, in case you are unaware. See, I got Chrysalis to laugh at you behind your back, and Nightmare has only made eye contact at me. I succeeded in making this boring takeover interesting!" Discord said as he continued to laugh. "You should've seen your face when we flew into the desert!"

Sombra snorted. The Changeling queen shook her head. "I was not laughing behind your back, in case you want me to make that clear," she said.

"Thank you."

"I was quietly chuckling at the cactus needles sticking out of your flank," she said.

Discord lost it. He continued to laugh as Sombra charged his horn. With a blast of dark magic, Sombra's one tooth turned into goo, and it was already melting. Discord stopped when he realized he was choking on his tooth. With a snap of his claw, his running tooth hardened and returned to normal.

Sombra smiled as Discord gave him a disgusted look. Then, he smiled as he realized that Sombra pulled a joke on the god of Chaos. Chrysalis smiled as she sipped her beverage. Her servant, the baby dragon Spike, had given her a tea found in Celestia's private kitchen. A kitchen, she later found out, filled with various cake recipes, including something called the MMMM. She had no idea what it was, but if Celestia were to return, she would go to this recipe. She hid it in the vegetable drawer in Luna's kitchen.

"Dear dragon, bring me more tea!"

"Yes mistress," Spike said.

Discord looked at the two interacting. While he made his choice to take Equestria over, he felt almost guilty of doing so in the first place. That small part of his mind screamed at him, telling him to go back and fix everything, but he knew that was impossible. All the ponies would rip him apart should he suddenly turn his back on them.

A bright light illuminated the room which they were all in. Nightmare Moon appeared, and she was not emitting an aura of victory. "Discord, you have some explaining to do," she said.

"Hot chocolate volcanoes were not my idea entirely. I found it enjoyable after a pony said that chocolate milk rain was not considered chaotic," Discord said.

"Not that! Wait, what?"

Chrysalis looked over at the god of Chaos. "Hot chocolate volcanoes?"

Discord shrugged. "It's a popular beverage in the winter, but its summer right now."

Chrysalis face-hoofed. "Anyway, I'm talking about the walls of Canterlot. There are a bunch of ponies out there calling for you."

Sombra raised an eyebrow. "Ponies know about you?"

Discord chuckled. "Yeah, um, I may've had some contact with the residents of Ponyville in the past."

Blood started to rush to Nightmare's head. "YOU SOFT-HEARTED FOOL! YOU ALLOWED YOURSELF TO GROW WITH THEM?!"

"Like I had a choice! It was either be released from stone and conform to them, or remain in my prison and you all would've never been here, drinking the golden drink that is victory!"

"I'm going to pretend you didn't compare our victory to a golden drink," Nightmare said. "Just get out there and deal with this!"

Discord rolled his eyes and teleported to the outer walls of the city. When he appeared before his pony citizens, he was almost nailed with an empty tin can. The can, somehow, was thrown with a stone in it. The draconiquus smirked at the weapon and looked over. It appeared as though all of Ponyville came to the city.

The god of Chaos scanned the city. He smiled as he noticed the Mayor of Ponyville leading the crowd. "Discord! Can you hear us?!"

"NO!" he responded.

Nopony cracked a smile. "Discord, we demand that you open the walls of the city! We want our princesses back!"

Discord laughed at the Mayor's demand. "And what will you do if I don't!"

"Then we will come in ourselves!"

Discord froze. That wasn't the Mayor. On the ground, ponies parted like the Red Sea, and two ponies took the front. One of them was Trixie without her magician's hat. The other was a pony with a snow-white coat and an electric blue mane. The pony wore a pair of magenta glasses and had a wild grin on her face.

The draconiquus smirked. "Trixie Lulamoon. I see you formally declined my invitation to the party. I see you also made your choice when it came to unlimited power!"

Trixie sighed. "Trixie made her choice a long time ago, Discord! Trixie chose her fellow ponyfolk over you gods! Trixie will not force her brothers and sisters to bow to her again, not after the Alicorn Amulet scandal that tarnished her image."

"You tarnished it a long time ago, Mediocre and Weak Trixie. Besides, what power do you have to burst through this wall?"

Trixie smiled. "This time, Trixie does not have the power to bust through. Trixie would like to introduce a pony who had a similar beginning as Trixie. Behold, the DJ Pon3, Vinyl Scratch!"

Vinyl cheered as her name echoed up the wall. "Thank you for having me, Trixie!"

"Trixie is honored to have you here!"

Vinyl laughed. Discord laughed harder, and that grabbed the pony's attention. "You brought a DJ to break these walls? Oh that's rich! What is she going to do, spin some tracks?!" he laughed at his own joke.

The DJ smiled. "Well, yeah. My friend Trixie, I need your help. I need the black suitcase that's back there."

Trixie smiled. "The Great and Powerful Trixie will fetch your black suitcase."

Discord laughed even harder. Trixie disappeared into the crowd, and later returned with the case that Vinyl wanted. The DJ thanked the magician as she set the case down. The draconiquus looked down at the case. It was a long and rectangular suitcase, and it looked like it weighed a ton.

The DJ smiled up at the god of Chaos. She unclicked the locks on the suitcase and waited for Discord to stop laughing.

He looked down at the DJ. "And what, pray tell, is that?"

Vinyl smiled. "Oh, it's nothing special—"

The lid flew open as Vinyl hoisted herself on two hooves. Using her magic, Vinyl lifted the object inside. It appeared to be a minigun you would see in videogames. It had two record players attached to both sides along with dual speakers. The barrel of the weapon was long and painted white like the owner. Using her magic, she locked two mechanisms to her hooves and held the barrel of the gun at the wall.

"It's just my Bass Cannon!"

With a flick of a switch, the weapon charged up. The two records on the sides started turning as a song began playing. When the bass dropped, however, the walls of Canterlot were blown apart. Discord and a few other guards were sent packing as the concrete wall caved in. Vinyl's newest track began playing as more of the wall fell.

Discord screamed as he flew through the air. Trixie reared up, kicking the ground and her horn charged up. "CHARGE!"

All the ponies in Ponyville roared in response, and they all stormed the city. Slowly following the crowd was the DJ continuing to fire her Bass Cannon at the structures within that were built by the Shadow Ponies. Discord teleported to safety, but he knew that nowhere in the city would be safe. He looked up into the sky, and it was filled with Pegasi flying in from Cloudsdale. The draconiquus did a double take when he noticed some of the Pegasi carried unicorns with them.

Without a second to think, Discord teleported back into the throne room with the other 3. Sombra screamed as Canterlot was quickly filled. Legions of Shadow Ponies and Changelings met with the rebellion, but were quickly overtaken by them.

Chrysalis immediately grabbed Discord. "You promised me victory!"

Discord raised his hands in innocence. Suddenly, a magical window opened in front of Sombra. _"Your Majesty, the Crystal Empire is under attack!"_

Another window opened in front of Chrysalis. _"Mother Chrysalis, Appleloosa and Ponyville has fallen. We request assistance!"_

Another opened. _"Mistress Nightmare, Manehattan has fallen! We need reinforcements!"_

Discord gulped hard. Chrysalis walked toward the window of the throne room. She watched as her Changelings were overrun by the ponies. She scanned the horizon, and her heart dropped. She could swear, that in the distance, a familiar blue box was flying through the sky.

And straight toward them.

* * *

><p><strong>AN: Almost done my friends. Only a few more chapters left, and **_**Dark Vengeance **_**will be complete. Please leave a review, follow, and favorite the story to show support. Follow me on Twitter sir_scribe for updates on future stories. Until next time!**

**-SirScribe**


	20. Taking Canterlot: part 2

**A/N: Greetings people of Fanfiction! SirScribe here with a new addition to **_**Dark Vengeance,**_** and I can now say that we are so close to the end of this story. I know, it sucks for me too, but this has been a very interesting project that I've been working on. This was the first MLP fanfic that I found to be spectacular. I have to thank, beyond anyone else, Tiarawhy for making the video that started it all. It's called Friendship Was Magic. Without that video, I wouldn't have made this, and I am glad to be writing for you. I will finish this story soon, probably before Thanksgiving so you got some more time to spend with the ponies in this little tale.**

**P.S. I'm rocking my BAD WOLF beanie right now, so I am feeling the power of Doctor Who right now. Haha, ok now the story shall progress!**

**Fluttershy: …um hello everypony**

**Me: Thank you for coming Fluttershy. I appreciate it.**

**Rainbow: Only because I'm here**

**Fluttershy: Well, it's not just Rainbow Dash. I'm sorry for running earlier**

**Me: It happens to everyone at some point.**

**Rainbow: Not me**

**Me: Don't. Anyway, Flutters, can you please give the introduction**

**Fluttershy: Um, ok. SirScribe doesn't own MLP:FiM. **

**Me: Thank you Flutters. Now then, let's rock and roll!**

**Fluttershy: ****Yay!**

**ONWARDS!**

* * *

><p>Twilight opened the doors of the TARDIS. The sheer mass of ponies storming Canterlot brought her to near tears. Not of sadness, but of happiness. Even though they possessed the powers of the Elements, there is no force in the Universe that rivals the will of those who are willing to fight for what they believe in. With Vinyl breaking down the walls of the city, the princess learned to never doubt the musical, or engineering, talent of the DJ.<p>

The Doctor held tight on the controls. His brown long coat was flying in the wind along with his goggles. He had sent Princess Luna and Ditzy ahead to find the Elements of Harmony before they arrive to the throne room. His hearts were still beating rapidly as the plan they all devised still raced in his mind.

_I am asking you all to trust me. Above anything, do not deviate from the plan, no matter what happens to me. This is your world, I am only helping you succeed,_ he told them earlier.

The Doctor smirked to himself. _Trust? Like that's going to happen._

Twilight turned back to the Time Lord. "Are you sure about this?!"

"Yes! If your theory is correct, then there shouldn't a problem!"

"Not about my theory, about you. Are you sure you can pull it off?"

The Doctor looked over. "Nothing is impossible, my friend. Just difficult to pull off. Ok, we are nearing Canterlot Castle. Applejack, do you have the rope?"

The farm pony looked up. "Ah got it!"

"Excellent. That rope is made of an industrial material that is very durable. Lasso the rope onto the spire of the throne room and take out the guards. You will need to hold on tight!" the Doctor said.

"And I have that, right?" Twilight asked.

"That's the idea. Now, Rarity and Pinkie, I've supercharged your cannons so they shoot more ribbons and confetti."

Rarity looked at the Doctor. "But I don't have a cannon," she said.

The Doctor smiled. "Today you do. I want the both of you to work together in taking out the guards. Once they are done, we move to the next step, and if they have the Elements by then, the night will end. Although, maybe it's supposed to be night right now."

"Let's not talk about that right now, Ok Doctor?" Twilight said.

The Doctor nodded. He then turned to Pinkie Pie, who was busy testing her brand new cannon. "Are you feeling Ok?"

"Yeah, why wouldn't I be?" she asked.

The Doctor said nothing and returned to the console. Waiting for him there was Applejack with her hat down. "And you?"

Applejack shrugged. "Ah never had a problem."

The Doctor gave her a look. AJ sighed as she put her hat down. "Ah'm still trying to come to terms with it. Are ya sure she won't forget?"

"Let me put it to you this way: cider season is celebrated by everypony, including the princesses. You won't be forgotten, none of her friends will."

Applejack smiled as she hugged the Doctor once again. Twilight looked over at Applejack. While she understood what Applejack's argument was, it was tough to digest the truth once spoken. Pinkie looked over at Applejack, then at Twilight, then back at Applejack. Before she could say anything, Rarity's hoof went to her mouth, keeping whatever Pinkie was about say in her head.

For now.

The Doctor looked all around. With Rainbow and Fluttershy leading the Pegasi through the air (Fluttershy was a surprise when she volunteered), the plan looked almost like it would work. If Ditzy and Luna get the Elements, then victory. With everything in place, the Doctor floored the TARDIS, which shot forward. Applejack readied her lasso while Rarity and Pinkie readied their cannons.

"Well then, Allons-y!"

Applejack had launched her lasso at the spire of the tower. With Twilight's magic, she was able to hold her friend down. With her strength and the Doctor's flying capabilities, they launched themselves around the building. Pinkie and Rarity approached the open doors and began firing.

Well, Pinkie did.

Rarity looked at the cannon she possessed. Except for the fact it was a weapon, it was neatly decorated with purple laces and ribbons. A series of gemstones were embezzled onto the barrel of the cannon in the shape of her cutie mark. On the top of the cannon was the trigger that appeared to reach whenever she pushed the button.

The fashionista looked at the Doctor, who was busy trying to keep the TARDIS from exploding. "But, I don't even like cannons! They're not in style, and they probably won't ever be in—"

A blast of green magic flew into the TARDIS and struck a curl on Rarity's mane. The unicorn watched as part of her well-styled mane became undone. Her eyes went wide as she turned her attention to the outside world. A few Changelings had clogged Pinkie's cannon with a green goop.

Rarity looked at her messy mane. "You ruined my curls!"

Applejack kept herself from laughing. The fashionista approached her cannon and slammed on the trigger. A barrage of confetti blasted out of the cannon and completely obliterated the Changeling's smile. They flew back as Rarity continued her attack while Pinkie removed the goop from her cannon. But Rarity didn't need any help from the energetic baker.

The Changelings needed help.

As Rarity continued to fire away at the Changelings, an alarm on the console began to ring. "Shadow ponies!"

"Can you fight them off?" Twilight asked.

The Doctor smiled. "There are a lot of things I do whenever I'm bored. One of those things is add a new modification to the outer lightbulb on the roof of the TARDIS. Just wait."

As the Doctor talked, three Shadow Ponies began flying toward the magical blue box. Their mouths widening with their fangs bared for all to see. The Doctor saw them on his monitor, but he did nothing. All he had was a hoof hovering over a blue button.

One of the Shadow Ponies screeched loudly, alerting the alicorn princess inside. "Doctor?"

The Doctor held his hoof high. The Shadow Ponies screeched again, this time striking fear into all the ponies in the TARDIS. "DOCTOR!"

The Time Lord raised his hoof. "FLASH BANG!"

His hoof slammed on the button. The light on top of the TARDIS immediately flashed a bright light. The Shadow Ponies shrieked as the light blinded them, and destroy their physical form. Their former magical bodies were wisps in the air now. The Doctor laughed as the screeching of the Shadow Ponies faded into nothing.

Twilight was impressed with the Doctor's work. He had managed to drive them away. With the last Changeling guard wrapped up like a Christmas gift, Applejack released the lasso. The Doctor walked toward the Comm station. "Rainbow Dash, Fluttershy, it's the Doctor. Return to the TARDIS, we're almost ready."

_Who was that?! _Came Fluttershy's voice.

_Ugh, we'll be right there. C'mon Fluttershy, he even said his name!_

The Doctor chuckled as he released the Comm button. He looked over at Applejack, who shook her head. "Ready?"

"Ready as ah'll ever be," Applejack said.

The Doctor smiled. A few minutes later, the two Pegasi returned and shut the doors behind them. The Doctor set the coordinates and the TARDIS dematerialized, leaving behind a city filled with angry ponies eager on getting their homes back.

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><p><strong>AN: Alrighty then peoples! Almost at the end of the story. Your support has kept this project going since day one, and I am happy for that. Sadly, this cannot go on forever. I'll be back later on with Luna and Ditzy (Derpy) running to get the Elements, and soon, Twilight and the Doctor's master plan will be revealed. Until next time, Flutter On!**

**-SirScribe**


	21. The Elements are back!

**A/N: Welcome back my friends! I'm going to try and keep the updates short now that the story is almost done. Just a few quick things. One, I am hearing throughout the brony community about a possible MLP movie coming out in 2017. I cannot say these rumors are true, but if they are, then AWESOME! Ok, I will say that I am expecting quite a bit from Hasbro, especially after the fall of the Hub Network.**

**Second, Rainbow Rocks rocked! I loved it better than the first, and I liked the first. The writers actually tried to get a story across, and it got me wondering about how time works between the two dimensions. Anyway, I will not say any more. You want to read a story, and I'm going to give you a story to read. Let's get started.**

**Disclaimer: I don't own MLP:FiM.**

**ONWARDS!**

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><p>Luna sighed nervously as she entered through the secret tunnel of the castle.<p>

The Doctor and Twilight both agreed at sending herself and Ditzy ahead to retrieve the Elements was the best thing they could do at this point. While she favored a full frontal assault, sneaking in through the back didn't pump Luna's blood the way she wanted it to. That didn't stop Ditzy from jumping right on it. With no resistance from the outside forces, Luna and Ditzy snuck through the gates and into one of the castle's many secret entrances.

Ditzy smiled. For the first time (well, first of many times), her derpy eyes came in handy. With both eyes in different directions, there was a slim chance of them getting jumped by any Shadow Pony or Changeling that may be hiding down in the tunnel.

Throughout their years traveling with the Doctor, Ditzy and Luna had gotten very well with each other. The two didn't see each other as princess and pegasus, but as sisters almost. The two shared many stories throughout their travels, including some of Luna's many adventures when she was a foal. Whenever Ditzy asked her about her parents, however, Luna spoke nothing. She would always say that she never had parents in the first place.

The gray pegasus didn't push her any further than that.

The two continued traveling through the tunnel in silence. Running through Luna's mind was the Doctor's plan, and it scared her. If they failed to retrieve the Elements, he would die. If they succeeded, he would still die, but the world would be saved. Luna had hope that the Doctor's plan works the way he wants it to.

That would mean putting her faith in Twilight as well.

"So—" Luna said.

Ditzy looked at the alicorn. "Umm, so how about those Wonderbolts?"

Luna gave her a funny look. "These Wonderbolts are strange contenders. What is their sole purpose?"

"Fly all fancy I think," Ditzy said.

Luna cocked her head in agreement. "My sister had too much time on her hooves to create a group of flying pegasi. Perhaps I will attend one of those Wonderbolt races," she said.

Ditzy smiled. They continued walking down the cave and eventually stopped at the end. There was a stone boulder in the wall. Probably they covered a hole. Luna reached to the boulder with her magic and attempted to remove the boulder. As she did, Ditzy continued to watch the tunnel behind her. She thought she saw something follow her. When she turned to find the thing, there was nothing there. She rubbed her eyes and returned focus to the boulder that Luna was trying to move.

With one more surge of magic going through her horn, Luna finally moved the boulder. With the boulder out of the way, the duo moved into the room. It opened to a simple bed chamber, probably a spare room for any guests. The door leading to the hallway outside was ajar. In the middle of the room was a blue cannon. Upon further inspection, Luna discovered that it was Pinkie Pie's Party Cannon. She probably left it behind the last time she was there.

Luna let out a curse. "We are far from the Element Tower. We're going to have to be very quiet when going through the castle," she said to Ditzy.

The pegasus sighed. "Quiet but quick?"

Luna smiled. "Quiet and Wonderbolt quick."

Ditzy smiled, and with their wings spread open, the two flew through the castle. Thanks to a pegasus's natural agility, the two were as quiet as the wind. There were some Changelings in the hallways of the castle, but thanks to Luna's Shadow Walker spell, they managed to continue without detection. Ditzy then considered what life would be like with magic.

She washed her brain with bleach after imagining it.

The two eventually arrived to the Element Tower. Luna and Ditzy clopped hooves with each other. Success. Luna opened the doors, and once she did, she felt her heart sink to the floor. Inside the chamber that harbored the Elements were a legion of Changelings and Shadow Ponies. In the very front of the group was Nightmare Moon, who was practicing her magic on a willing Shadow Pony.

The Queen of the Dark looked up at the duo. "So, the rumors are true. Princess Luna of Everfree and Derpy Hooves are here to save the day. How adorable," she said.

"Ditzy!" the pegasus exclaimed.

Nightmare growled at the wall-eyed pegasus. "I was hoping for a real threat, and while you have Chrysalis and Discord on edge, I can assure you that I will not submit to legends. The cavalry in a flying blue box? Yeah, not the biggest threat to this new empire."

"Empire?" Luna pondered.

"Yes. I am the ruler of the Night, Discord is the god of Chaos, Chrysalis is the Head of Military, and Sombra is King of the world. I must say, it worked out well, this idea of Discord's. Now, will you submit to myself and the empire, or will I have to destroy you?"

Nightmare took a few steps forward, but Luna stepped in front of Ditzy. Luna's horn was charged up and ready for anything.

The Queen of the Dark smiled. "Care for a rematch, Luna? Or are you going to surrender as you did almost 1,000 years ago?"

"Trust me, there won't much of a rematch," Luna said. With that, she fired an arc of magic at Nightmare.

Nightmare raised her wings to block the spell, but when it made contact, the queen of the dark was sent flying back through the air. She landed at the door of the Elements, squishing a Shadow Pony in the process. The crowd was now rowdy as they awaited their queen's orders.

Nightmare rose to her hooves. "I WILL NOT SUBMIT TO YOU!"

The alicorn flew through the air. Luna had her horn charged, and when Nightmare came close, she raised a shield. Nightmare's momentum forced her to go flying back once again, but she recovered in the air. The Changelings and Shadow Ponies were not to sit by any more. They all rose up and charged at the duo.

Luna raised her shield again. Over a hundred magical bolts and shadows came at her with full force. Luckily for the alicorn, she learned greater defensive spells that proved to be greater than any in her personal spell book. Once the Shadow Ponies fell back, Nightmare came charging back.

Luna grinned. She flew up into the air, and Nightmare followed. Blasting a hole through the roof, the two alicorns fought for control of the night. The Changelings and Shadow Ponies all gawked at the queen of the dark disappear, and once she did, all eyes fell on the wall-eyed pegasus.

Ditzy looked at the army of foes in front of her and whimpered. They all growled at her and began to slowly advance. Ditzy started moving toward the exit, but they weren't going to have that. Several Shadow Ponies formed behind her, and when she noticed, Ditzy had no choice but to move to the stained glass windows behind her. One of the designs was of Princess Twilight emerging from a lotus, possibly symbolizing her rise to the title of 'princess'.

Ditzy's rear hit the glass. She was going to be swarmed by the demons advancing. She covered her eyes, waiting for them to attack.

_Dear Ditzy Doo, whatever shall you do?_

The pegasus looked up. She heard that voice clear as day. None of the Shadow Ponies seemed to have been bothered by the voice. She searched for the source of the voice that spoke with the caring of a mother.

_Please Ditzy Doo, remember the power in you. With eyes beyond and loopy, one may not expect one's eyes so droopy._

A fire ignited within Ditzy's stomach. Her sight straightened for one moment, and the whole room was engulfed in a bright light. The light didn't bother the pegasus, but she heard the screaming and cursing of Changelings and Shadow Ponies.

When the light died down, Ditzy had to do a double take. Every single Changeling and Shadow Pony had wall eyes. They all stumbled around, trying to focus on their target. Soon, some fell over while others fired wrong spells at the wrong targets.

_Go Ditzy Doo,_ came the voice.

"Whatever you say, random voice in my head," Ditzy said. With a wide grin on her face, the pegasus soared above the crowd of confused Changelings and demons. The door glowed as she approached it. For the first time ever, she was going to do something right.

* * *

><p>Sombra looked out the window and sighed. The empire he worked so hard to build was already starting to crumble before his eyes. Chrysalis was having a panic attack over the box she saw, and Discord was trying to stuff all the clown puppets back into their spring-loaded boxes. The Draconiquus, while he appeared calm, was breaking down inside.<p>

_I promise you all absolute victory. Without their guardian Elements of Harmony, nopony will think about rising against us,_ he promised them the night they met. _Before this month is done, this world will be ours._

Boy did he screw up big time.

Sombra loked over to see Discord practically not giving a pony's plot about the situation. "DISCORD!"

"I'm howling at the Moon!" he responded.

Sombra face-hoofed. "You idiot, you promised us victory! Nay, you promised ultimate victory!"

Discord sighed. "Breaking up the Elements may've backfired on us, but we still have one missing Element. Even if those ponies survived, Twilight would not able to rally them up. This rebellion is only because—"

"Somepony organized a global revolution, Discord! You cannot say this is a random occurrence. My Crystal Empire has fallen, Nightmare Moon's power has faded, Chrysalis is having a panic attack, and I'm here shouting at you for being a complete nutcase! Please do not say that this was randomly organized!"

Discord raised a claw to speak, but no words exited his mouth. Sombra sighed and continued to watch the rebellion unfold. Discord shrugged and continued his chore when it happened.

As Chrysalis calmed herself, there came a whirring sound. All ears turned to the entrance to the throne room. A light began to materialize along with what appeared to be a blue box. As the sound grew closer, the box began to take form. It was a large, blue box with a light on the top. The box had a set of doors with windows glowing white.

The sound ceased, and the box came into existence. Chrysalis backed away from the object in front of her. The door opened, and stepping out of the door was Rainbow Dash and Applejack. Behind them came Pinkie Pie, Rarity and Fluttershy. They all stepped out with serious looks plastered on their faces.

Without warning, the 5 ponies moved in. They all shouted as they got close to Sombra. Thankfully for his quick thinking, Sombra fired a Freezing Spell on them. The five ponies found themselves frozen in place in the middle of their battle cry.

Sombra chuckled. "So this is the reason why the whole world is suddenly resisting us. Glad to know that my Number One commander deserted her post to rebel against me," he said.

"And my servant decided to leave Appleloosa with only half the job complete. In a way, I saw this coming," Chrysalis said.

Discord said nothing. He was in the middle of a scolding from Fluttershy, the one pony who believed in him. While he was completely on board in taking over Equestria, he expected it to be quick and painless, instead he got this. The feeling of betrayal loomed over the Draconiquus.

Sombra smiled. "Now it appears I have no choice but to eliminate you all. Which one will go first? Will it be the loyal Rainbow Dash?"

His horn moved to the cyan pegasus, who growled at the King of Shadows. "Or the Earth Pony who burns with a fire that can outlast Equestria?"

Applejack faced his horn. "Perhaps she will go first."

Before Sombra could conjure the spell, the magical hold on the five. The door opened again, and stepping out of the TARDIS was Twilight with her wings high in the air and her horn charged up. As she walked by her friends, they all stood on all hooves and ready to fight.

Chrysalis was immediately confused as to Twilight's return. She fired a spell that should've killed an alicorn. Discord, while visibly distraught, felt relief. At least he didn't have a dead princess on his conscious anymore. Sombra, out of all of those in the room, was the most surprised. His heart began to beat faster than it was supposed to. "But-but you're supposed to be dead!"

"So you didn't bother looking for my body?"

Sombra immediately scowled at Discord. "You said she was dead!"

"No, I said she was gone. I said nothing about 'dead'."

The coil in Sombra's brain snapped. "THAT'S IT! I'LL DESTROY YOU ALL, STARTING WITH YOU, TWILIGHT SPARKLE!"

He charged his horn and fired a beam of dark magic. Twilight immediately raised her magical shield, redirecting the beam into the ceiling. Chrysalis snapped out of her fear and fired a magical blast along with Sombra. Twilight smirked as she deflected both. Discord snapped his claw and a chain appeared from one of the boxes. He ordered it to attack Twilight, but she easily released it from his magical grasp.

As Twilight dealt with Discord, Sombra smiled. He charged his horn, and with Twilight's attention on the Draconiquus, he made his move. He fired his killing magic blast at the alicorn. Instead of hitting its target, it hit something else. A body hit the floor and everypony in the room stopped. The sound echoed through the throne room, and the only sound that existed was the sound of a heart speeding up. In front of her was a brown Earth Pony stallion.

"DOCTOR!"


	22. The storm touches down

**A/N: Greetings people, and welcome back to Dark Vengeance. I hope you all are having a great morning/afternoon/night, and if you're not, then continue reading this fic. You know what, if you're happy or sad or everything in between, read this fic anyway. Haha, I have been anticipating this chapter ever since I made Doctor Whooves and Ditzy appear in this fic. I will be also updating **_**New Life in Ponyville,**_** but that will be the end of it. This will finish, and then, **_**Whooves N' Jack**_** will continue on my other account. I have thought about keeping this account active, but after a bit of thinking, I've decided against it. I might go back on my word again, but if I do, then expect some good fics from me.**

**The gang is taking time off. They finished with the finale for season 5 so they're resting right now. They said it will be released soon, so be ready for more ponies. I know I am. Anyway, let's rock and roll!**

**Disclaimer: I'm not Lauren Faust, so I don't own MLP:FiM. **

_**Allons-y!**_

* * *

><p>The 6 stood over the Doctor's lifeless body. For a split second, Twilight didn't see him coming. She was facing against Chrysalis when Sombra attacked. If he didn't do anything, Twilight would be dead for real, and Equestria would fall for good. He had told them of the plan, but she didn't expect him to jump in front of her like that.<p>

_This pony is insane!_ Twilight thought to herself.

Sombra, on the other hoof, was trying so hard to resist finishing all 6 off at once. While he was eager to regain control, he wanted them to accept what happened to the Doctor. Might as well break their spirits before they were obliterated. Chrysalis still had fear in her eyes, but she was not focused on the lifeless Doctor. Her focus was on the blue box in front of her. She recognized it from a painting back in the Badlands. It hung from Chrysalis's lair where she would stare for hours, wondering why she was fearful.

Discord looked upon the 6 with concern. His plan called for separating the Elements of Harmony and a clean takeover. He didn't plan for death and destruction. While he was chaos, even he had guidelines when it came to something like this.

Twilight and Rainbow looked up. "YOU MONSTERS!" Rainbow bellowed out.

Sombra smiled. "A pawn that needs to be taken in the game. I have you in Checkmate, Princess Twilight. You cannot fight, not without the Elements of Harmony. Submit to us, and you all will not share your friend's fate."

The 6 looked at each other. Instead of backing down, the 6 stood together behind the Doctor. Sombra smiled. "Then I guess we will be legend after all. Behold, Discord. Tonight, the Elements die!"

Instead of answering, Discord cried out. They all looked back at him. His snake-like form was spasming like he was getting the chills. His eyes glowed gold before he managed to calm himself. Sombra looked at him with concern. "What is the matter?"

"I don't understand. There is a great magical disturbance in two different places happening at the same time. One in the Element Tower, and the other—"

"Where?"

Discord looked up at the lifeless Time Lord. "There."

Everypony turned their eyes to the Doctor. Without warning, the ceiling caved in. Falling from the sky was Princess Luna. She was battered up like she was in a fight. Appearing next to Sombra was Nightmare, who was missing her helmet. She was scrapped in several places, especially around the face, but she was in better condition than Luna. "They entered the Element Tower. We have our children holding it against the pegasus intruder. She will not get the Elements. Now, what is the problem here?"

Sombra sighed. "Discord has sensed a magical disturbance where the brown pony lies. He is dead, Discord! There cannot be a magical field around him," he said as he glared at the draconiquus.

"But I am serious about this. I'm picking up a surge of energy coming from that Doctor guy," he said.

Chrysalis smiled. "You are probably picking up his soul leaving this world. There is no way that he—"

A struggled groan broke Chrysalis's thought. The 4 looked over, and picking himself off from the ground was the Doctor. As he rose, a look of disbelief formed on Twilight. He took a serious magic curse for her that should've killed him. Once he was on all four of his hooves, he brushed off his forelegs like he rolled in the dirt. In the center of his chest was a burn mark.

Sombra was in disbelief as well. "But-but that was my most powerful spell. It's supposed to be enough to put down an alicorn!"

"Then I have a lot of questions for you, but first I must say: by all the stars in the sky did that hurt! I've felt a lot of pain in my days, but that hurt beyond everything else. Mainly because I've managed to cheat death for about 30 years or so. Yeah, that will take a lot more energy than I would've wanted to use." He turned to the 6. "You all OK?"

All the ponies nodded their heads. "Sorry for scaring you like that, but if I mentioned doing that, you all would've tried to stop me. This is the only way I can help," he said.

Twilight shook her head. "That was the most reckless thing I've ever seen!"

"Darling, you have a serious mark on you from that magic blast," Rarity pointed out.

He smiled. "Want to see a magic trick?"

The Doctor took a deep breath. He moved his hoof over the mark, and as it brushed over his fur, the mark disappeared. He took a deep breath as he calmed his hearts. "Feel better now?"

The 6 said nothing. He shrugged to turn back to Sombra. His horn was charged once again. "How did you do that? You're just a regular pony!"

The Doctor turned to the TARDIS. "Can regular ponies pilot the TARDIS? Well, if I teach said regular pony, then the answer is yes, but disregarding that, the answer is no. And I am not a regular pony! Regular is boring!"

Chrysalis looked on in fear. "That box, what is it?"

"It's called the TARDIS. It stands for Time and Relative Dimension in Space. It can travel anywhere in time and space, and it's mine," he said.

Applejack looked back at the TARDIS. _Time machine?_

Nightmare laughed. "Time machine? That is impossible, even with magic. Starswirl only completed one small spell to travel in time and that only works for a short amount of time. It is impossible."

"Nothing is impossible, just difficult to complete."

The Doctor fixed his stance. "I just find this all amusing that you have gone through all this just to be stopped by 6 ponies," the Doctor said.

Nightmare laughed. "Us? We overpower those puny ponies. Separate, we don't stand a chance against you all, but now with our assembled powers, you 6 will be destroyed!"

The Doctor smiled. "That is all I needed to hear. You threatening to destroy them, my friends, will not sit kindly with me. You don't want to see me when I am determined to keep the ponies I care about safe. You have no idea what you are getting yourself into," he said.

Sombra smiled. "You are trying to sound brave, but I smell fear on you. As the lord of fear, I can sense if ponies have a particular fear. You have monsters you don't want to resurface. 10 monsters are rising, Doctor, and I will gladly work with them to ensure that you will never raise your head again!"

Sombra reached out with his magic, grabbing all the minds of everypony in the room. Discord, feeling left out, pulled a wire out of thin air and plugging into Nightmare's horn. The alicorn gave him an odd look as he shrugged it off. Even the Mane 6 was plugged into Sombra's mind. The unicorn approached the Doctor, who was standing tall. "Let's see what this Doctor fears, shall we?"

The rest of the 4 agreed. Sombra's horn touched the Doctor's forehead and the room was engulfed in a green light.

Instead of one pony screaming, there were 4 screams. Sombra and the rest of the 4 screamed in terror as the visions entered their minds. In them was a tall, hairless ape. The visions showed at least one of the creatures, but they all were different. One wore a strange brown hat and scarf, another wore a white jacket with a celery stalk pinned on it. One wore a leather jacket and held a silver stick with a blue light. With a press of a button, the vision changed once more.

The Doctor forced the last image into his mind. It was the image of a tall man with a brown suit and jacket. He had spiky hair and he was the Doctor. He stood in front of an army of various creatures, all appeared to be in metal. Giant creatures in suits of armor, mysterious egg-like creatures with eyestalks, and many more monsters.

"I am not just a regular pony! I am much more than just a regular pony! Entire armies have turned and ran away at the mention of my name!"

The Doctor in the image took one step forward, and the army of monsters immediately turned and ran. Some tried to fight back, but the Doctor would not fall. So many of the creatures fired what appeared to be magical blasts at the Doctor, but he simply dodged them. Raising his screwdriver, the Doctor pressed the button. The remaining monsters turned to ash and dust.

"I am the survivor, nay, the winner of the last great Time War! I watched two almighty races burn and turn to dust! I have topples gods, raised empires, and burned stars with the words of my people!"

An image of a planet entered their minds. The planet burst into flames. The scene was enlarged and a vision of an elder man appeared to be shooting fire from his hands and face. As the fires rages, the man let out a blood-curdling scream. Entire structures fell and the egg-like creatures seen before were screaming in pain as the fires rages.

Twilight couldn't believe what she was seeing. The Doctor was endless. His power in this new form seemed to surpass his power now. "I will not stand idle while you destroy this world. As the last of my species, I will never allow you to win!"

The vision died in everypony's minds. Sombra looked up, and the Doctor was starting to emit golden smoke from his hooves. "But-but you still don't have the Elements. We are still more powerful!"

Right as he said that, they heard a mare call his name. "DOCTOR!"

The 4 looked for the mare. It was Ditzy with a chest full of the Elements. Ditzy dropped the box off in front of Twilight, who gladly opened it. "Sorry Sombra, but it looks like this is Checkmate," she said as she grabbed each of the necklaces.

"Time to get this party started!" cheered Pinkie as her Element was placed on her.

"YEEEE HAWWW!" cheered Applejack.

"Yay!" Fluttershy cheered.

"Well it's about to get beyond 20% cooler," Rainbow Dash said.

"This has gone on far enough," Rarity said.

With all the Mane 6 with their Elements, Twilight's crown began to glow along with the others. The five Elements started to emit magic to Twilight's. The cracks on the jewel began to disappear in front of the 4, who were now struck with fear. The Element of Magic was now fully healed.

Sombra shook his head. "What are you?"

"I am not just a pony. I am a Time Lord! I am the Doctor! I am 904 years old! I come from the planet Gallifrey in the constellation of Kasterborous. I am the Oncoming Storm, the Bringer of Darkness and your worst nightmare! Now it is time to say goodnight Sombra."

The smoke completely engulfed the Doctor. His brown coat began to glow gold. "Well then, ALLONS-Y!"

With a swift motion, the Doctor rose on his hind legs. His entire body erupted into flames as Sombra screamed. Twilight started to feel the magic of the Elements take over. With her friends behind her, she was ready. The 5 fired beams of concentrated magic at Twilight, who fired them at the Doctor. The flames of his regeneration started to move toward the 4, who were paralyzed in fear. The flames engulfed the 4, and the screams of the former rulers of Equestria echoed through the halls.

Sombra was first. He looked down at his hooves, and he noticed that they were cracking like glass. Before he could say another word, his entire body exploded and reformed. His horn, the only thing that remained flew toward the ground. The broken pieces of the King of Fear began to turn into stone around his horn. The pieces created a stone pedestal and an octagon piece with Sombra's horn in the middle.

Discord screamed as he felt his form cracked, but as he was about to explode, he felt time stop around him. The flames no longer burned his skin. The world became silent. The draconiquus looked around, wondering why the world became silent and still. Out of the corner of his eye, he spotted a pony wearing a giant blue hat and cape. His coat was white and he had a long beard that touched the ground.

_Not here, Discord. Your destiny doesn't end here. You are required for much bigger events. Escape now!_ The pony commanded.

Without arguing, Discord vanished into thin air. The pony in white fired a magical spell into the air, hitting everypony on the planet. Once the spell was performed, he vanished, restarting time. The flames continued to rage around Nightmare and Chrysalis.

Chrysalis turned to Nightmare. "You promised me victory, Nightmare Moon! You promised!"

Chrysalis' form cracked and exploded. For her mark, the image of a chrysalis took the center of the octagonal stone piece. The statue was near completion.

Nightmare screamed before her last words echoed through the halls. "YOU WILL ALL PAY FOR THIS! I AM NEVER TRULY DEFEATED! EVERY DREAM HAS A NIGHTMARE!"

With those last words, Nightmare Moon's form cracked and exploded. The crescent moon, representing her cutie mark, flew into the statue as the third and final octagonal piece built around it. The statue consisted of the three symbols of those who were defeated. Once the flames of the Doctor's regeneration died down, the Time Lord crumpled to the floor. He was the same as he was before the regeneration. His coat still that chocolate brown that he grew accustomed to.

Twilight smiled as the Elements finished the job, but it wasn't over. The world was still shrouded in eternal darkness. With the power still running through their veins, the Mane 6 burst through the ceiling and straight into the sky. Their charged forms left a trail of magic behind them.

The Doctor awoke from his regeneration. Without a second to assess the situation, he turned to his earpiece that he kept hidden. "Cadence, Shining Armor, do it!"

In the Crystal Empire, the royal couple had a group of ponies surround the Crystal Heart. Pouring their magic and love into it, the Heart began to awaken once again. It spun at a rapid pace, and with Cadence's last bit of magic, the Heart exploded with magic, shooting a ray of magic into the sky. The beam diverted toward Canterlot in the south.

The Mane 6 saw the beam from the Crystal Heart coming toward them. Focusing their magic into the spell, both the Mane 6 and the magic beam collided and lit up the sky in the biggest Sonic Rainboom in existence. The explosion rocked all of Equestria at the same time.

In Canterlot, Trixie and the main cellist, Octavia Melody held back the Changelings and Shadow Ponies. When the explosion came above them, everypony stopped fighting. The Rainboom ran above the city, and behind the initial explosion, the sky cracked. Behind what appeared to be the magical barrier was sunlight. A Shadow Pony happened to be standing when the light hit it. It screeched in pain as it evaporated into thin air.

All the Shadow Ponies went into panic mode. They all attempted to escape the sunlight, but the sky was cracking faster than they were running. Shadow Ponies by the millions around Equestria began to evaporate due to the sunlight. Changelings also managed to escape, some turning into regular ponies to escape prosecution from whatever was going to hunt them down.

As the sun shined throughout the land, the Doctor and Ditzy smiled. With the sun hitting his face, the Doctor shut his eyes. Exhaustion swept over him as he fell asleep.

The storm was over.


	23. Aftermath of the war

**A/N: Greetings everyone and welcome back to **_**Dark Vengeance**_**. I took a little bit of time off to get some things wrapped up. School is picking up and I need to get 3 essays done by next month at around this time. Yeah, 3 essays all at least 4 pages long. I can do that easy with my hobby of writing everything (I haven't tried writing clop) but the thought that they will be graded will be impossible. Anyway, I am glad to return. It's been a year since Season 4 started up and I am glad to say it is officially a full year since I started watching the show. Still got no cable to watch new episodes, but that's where the Internet comes in. Haha, ok that's enough.**

**UPDATE: I'm almost done with using this site for fanfiction. I will be on fimfiction though so I'm still working. Thank you again for all the support you have given me these past few months. I have a finale for my MLP fanfiction career planned out already (gotta decide which one to do) but I will be writing for at least another year or two. Oh boy.**

**If you like Percy Jackson and the Olympians and follow my other account, which is Newage416, then I am sorry to say that those stories that haven't been complete are canceled. I'm sorry my fellow demigods if there are any out there.**

**The 6 are gearing up for the Running of the Leaves race followed by the fall festival. They told me Nightmare Night went off without a hitch and…hey. Another story idea! I may be late on it, but its fanfiction. You can write in any time. I'll get back to you on the future of this account.**

**Disclaimer: I am not Lauren Faust and I am not a part of Hasbro. Therefore, I don't own MLP:FiM. I am also not a part of BBC, so I don't own Doctor Who.**

**ONWARDS!**

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><p>The sound of the Doctor's Sonic Screwdriver and intense headache jolted her from her sleep.<p>

The last thing Rainbow Dash remembered was the Doctor shooting golden flames from his body and Twilight charging the Elements. Once again, incredible power surged through the cyan pegasus as Twilight fired the one spell the Doctor told her to conjure: the Reversal Spell. While she didn't care so much about magic, Rainbow found herself grabbed by the Doctor's plan to take down the Shadow Trio. While he left behind the detail that he had to die, the plan was Rainbow Dash approved.

The cyan pegasus slowly opened her eyes. She was in the throne room of the castle. The stained glass windows were all shattered, there were three burn marks in the floor, and standing close to the throne itself was a small statue. The statue was divided into three parts, each represented by an octagon. Next to the statue was the Doctor with his Screwdriver in his mouth and Ditzy next to him. They both looked like they were studying the statue.

RD tried to rise to her hooves, but her body felt like lead. Her wings were tired from doing something. She wasn't flying in her sleep again, right?

Before she gave up and fell back asleep, she felt an aura of magical energy engulf her. She found herself rising to her hooves and her energy restored. In front of her was Twilight, who looked beaten up as well. She had scratches covering her entire body and bags under her eyes.

"Good thing you're awake," Twilight said.

Rainbow smiled. "You interrupted my nap, but seeing that we beat those jokers, I say I forgive you," the pegasus joked.

Twilight laughed and they hoofed. "Are the others awake?"

"Yeah, but they've been awake for a while. It took a while to wake you up though. I didn't know your coat turns white when you get too tired," the alicorn said.

Rainbow froze. "White? My coat is blue, not white!"

"But it was—nevermind. I don't want to know. Next thing I know, I'm asking Pinkie why she has wings under her coat."

The two friends laughed, but stopped. They both looked over to Pinkie, who was bugging Luna about wanting to see the castle on the Moon. RD had to do a double take because she remembered Luna crashing through the ceiling thanks to Nightmare Moon. She was laughing when Pinkie started showing her the signature Party Cannon. Wait until Pinkie wants to fire it.

"53!" they heard the Doctor said.

Both ponies turned to the Time Lord. "What?"

"Time locks. 53 Time Locks are in place inside the statue. I didn't think about Time Locks being implemented but it got the job done," he said. "Oh, and welcome back to the world of the living. I didn't expect you to take charge of the Rainboom like that RD. That was cool to watch."

"Huh?"

Twilight smiled. "I was awake for it. We shot straight up into the air and did the biggest Sonic Rainboom I've ever seen. It broke through Nightmare's spell like that baseball when it broke through my kitchen window," she said with a glare at RD.

"Can you quit bringing it up?"

The princess of magic shook her head. "Anyway, I got Spike to get Princess Celestia. Hopefully he didn't get lost."

"Are you sure the poor darling isn't still at the doors wondering why it's bigger on the inside?" Rarity asked.

"Ah'm still trying to figure it out mahself," Applejack said.

Rarity agreed. Twilight looked back at the TARDIS. Perhaps her little dragon was still in shock from it all.

The doors suddenly opened. Spike was walking out with Princess Celestia behind him. She looked weary and most of her horn was still broken. It was better than before, but magic was still off limits for the alicorn princess. Before she moved her hoof, Luna was already running to her sister. She embraced her sister in the biggest bear hug in the history of bear hugs. Celestia's yelp of pain and surprise didn't stop Luna from squeezing.

Twilight smiled. She was going to have to find Cadence and Shining Armor and do the same thing. Maybe it can be a family night. Or brunch. Maybe a late lunch/early dinner thing.

The alicorn shook the idea out of her head. Maybe later.

The Doctor walked up to the princesses. "I think Celestia wants to breathe sometime soon," he said.

Luna sighed and let her sister go. She mocked suffocating and gasping for air for the amusement of the ponies of the room. "Oh Doctor, the legends are very true. You do leave a mess wherever you go," Celestia said as she surveyed the room.

The Time Lord chuckled. "Wasn't me this time, or was it? No, I was regenerating. Oh, and be careful with that statue over there, it has the three fake gods in there," he said.

The princess of the Sun looked at the statue. "Why am I not surprised?"

Pinkie jumped up. "Because you know the Doctor?"

"Just about right, little one. Well, there is a lot of cleaning up to do. Why don't you take the statue to the catacombs of the castle, Doctor? We can clean this place up."

The Time Lord nodded. "Ditzy, help with the clean up."

"Okie-dokie," she said.

The Doctor grabbed the statue with his mouth and walked out of the throne room. Celestia sighed. "Where's Discord? He needs to help with the clean up."

Fluttershy smiled. "I'll go get him."

"No, he should come here. There is no telling where that draconiquus is hiding. Discord!"

In a flash of light, a small box appeared in the middle of the room. The box started to play a song, and when it ended, Discord sprung out like the joker in a Jack-in-the-Box. He wore a jester hat and held a flower as a staff. Celestia shook her head.

"Somepony call my name?"

"Yes. We need you to help with the community to rebuild. I'm not sure if you heard, but Sombra tried to take over Equestria with Nightmare and Chrysalis."

In the back of Discord's mind, a red alert flashed. _They don't remember me!_

The box disappeared and Discord reappeared with a reflecting jacket and hard hat. "Just don't let the pink one near any power tools and you got yourself a deal."

Twilight looked up. "Power tools?"

The draconiquus waved it off. He glared at the TARDIS. That Time Lord and his box ruined his plans again. He disappeared again, probably to either take a nap of search for the three idiots who took his plan too far. Once he was gone, Twilight shook her head. "Who knows what he was doing while Sombra was here?"

None of the ponies answered. "Maybe he was trying to fight him off?" Fluttershy said.

"I'm sorry darling, but isn't Discord stronger?" Rarity asked.

Celestia nodded. "We shouldn't focus on Discord right now. Twilight, I want you to properly secure the Elements. Sister, I'm going to need some rest and hopefully I can heal faster. Can you take my place—"

"We can gladly take thy place in supervising the clean-up and help with the reconstruction," she said.

Celestia chuckled. "Very well Luna."

The girls all cheered and ran out of the throne room to start with the clean-up.

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><p>It felt like weeks since the night ended and the clean-up began. Ponies all over were cleaning up the propaganda and banners left behind during what the Doctor called 'The Shadow Rebellion'. The statue was placed in a high-security chamber deep underground. The room itself was sealed in magic and a Time Lock, making it impossible for the three to escape. Discord could never find his three fallen comrades and gave up on the plan altogether. Nothing was going to happen with the Doctor around.<p>

Speaking of the Doctor, the Time Lord and his companion stuck around and treated Celestia while she was healing. With some more Time Lord sciences and medicines, her horn almost completely grew back. The exposure of her Magic Core, observed by the Doctor, was no longer a threat, but her magic was weak. She would need more time to regain her lost energy. That didn't stop Luna from taking control of the Sun and Moon while she was ill.

Finally, after a month of working cross Equestria, Canterlot was back to being the capital city. Princess Cadence reported that the Crystal Empire was back at full power and the Crystal Heart was shining bright. Ponyville and many cities were shining bright thanks to the leadership of the Mane 6. It was so great in fact that the Equestria Games were to continue in the Empire.

On a bright Saturday afternoon, exactly a month since the end of Sombra's brief reign, Canterlot was busy. Princess Celestia had called for a celebration to honor the heroes who defeated the royals of the Shadow Rebellion. The celebration was to be held in Canterlot castle with Cadence and Shining Armor attending. The whole city was the center of the world.

Inside Canterlot castle, Princess Celestia and Luna stood in front of a crowd of hundreds of ponies. Outside in the gardens, thousands upon thousands of ponies were ready for a whole 24 hours of celebrating. The Galaxy Watch that was put off would be one of the many night-time celebrations. Luna was elated.

The crowd of ponies fell silent as the trumpets blared, calling for their attention. Princess Celestia and Luna extended their wings.

"Fillies and Gentlecolts, I am glad that you all could attend. Today, we honor the ponies who fought against the world's worst demons to ensure that we live in peace. Today, our heroes will be rewarded for their efforts. Please join us as we welcome our heroes: Twilight Sparkle, Rainbow Dash, Applejack, Rarity, Fluttershy, Pinkie Pie, Ditzy Do and the Doctor!"

As their names rang through the halls, the doors came open and the 8 ponies came walking out. Ditzy and the Doctor smiled as they greeted the crowd of ponies, but the Doctor knew that this wasn't meant for him. All he did was drive the heroes around and sacrificed himself to correctly perform the spell that saved Equestria. It wasn't him.

Twilight felt her soul lift up. It felt good to finally celebrate after a month of working to rebuild. She looked over at her friends and took a mental note to never forget that friendship is a powerful magic that can carry anything over the most impossible thresholds.

The alicorn found herself staring at Applejack. She told the truth about what she thought of her new status, yet she appeared to be calm.

They approached the steps to Celestia and Luna's thrones. They both looked proud. "These ponies have demonstrated feats of great strength during the darkest days of our history. The proved to us that if we set our sights on a particular goal, and we work hard, we can accomplish anything."

Celestia magically produced a small chest. Inside was 9 golden medals. She placed all the medals onto the ponies before her. Even Ditzy and the Doctor received medals for their involvement. Once the medals were distributed, Luna looked back in the chest.

She turned to Celestia. "Sister, there is one more medal in the chest," she whispered.

The elder sister smiled. "I know."

She turned to the crowd. "While these 8 ponies worked on the front lines, I cannot overlook one more hero. This hero risked her own safety multiple times to ensure that her friends get their work done. Without her, Twilight Sparkle and her friends would not be here today and the Sun would not be shining."

She raised the 9th medal. "I take great pride in bestowing this medal on my sister, Princess Luna."

Luna turned in shock to her sister. Celestia smiled at her young sister. "While I was healing, it was my sister who stuck by me and ensured that my health would worry her less. It was also because of her that Twilight Sparkle is here. She saved her life, and that is great itself."

She pinned the medal onto her sister. "My sister has kept Equestria in balance and maintained power. I am very proud of her."

Twilight smiled. "Behold, citizens of Equestria, your heroes are here!"

The ponies started to cheer. Luna smiled as she looked down at her medal. She had something material to be proud of.

The Doctor and Ditzy cheered for their friends and their accomplishments. The Doctor kept a note in his mind saying he should check up on the 6 in the future.

All the cheering ceased immediately. The noise in the room was replaced by the sound of cloister bells. The Doctor immediately recognized that sound. He slowly turned back to the doors, and under the archway was the TARDIS. The doors were wide open and the interior was blanketed in a red light. All the ponies in the room began muttering amongst themselves. Celestia and Luna were shocked at the time machine's sudden interest to join the celebration.

Ditzy, on the other hoof was more interested in the stained glass windows above the two princesses. "Doctor?"

The Time Lord turned around to face the windows. With one glance, he gasped. Written on the windows were the two words he dreaded to see: BAD WOLF. The words were written in red. Everywhere he turned, the same two words rang in his head. Ponies started to freak out at the sudden appearance of the words. Some got the idea it was written in blood.

The Doctor's two hearts started to beat faster as he processed the words. The hairs on the back of his neck stood up as more ponies started to freak out. One pony screamed louder than everypony else. "There's a wolf in here!"

The Doctor turned around, and standing in front of the TARDIS was the Bad Wolf itself. The wolf was sandy-colored with golden eyes. It sat patiently in front of the TARDIS. _Hello Doctor, long time no see._


	24. The Doctor rises

**A/N: Welcome back my friends, and welcome to **_**Dark Vengeance. **_**Well, this is pretty much done. I have the epilogue done already, but I'm going to make some changes to it before uploading. Thank you again for the support and reviews. I know I've had some rough patches in early chapters but you cannot progress without some problems. For those of you who do not know about the BAD WOLF, the BAD WOLF is a creature that appears throughout series 1 of the revamped Doctor Who. The BAD WOLF is a self-created creature that had the Universe in her head. She burns like the Sun. Sorry if I confused some of you. With that in mind, let's get this wrapped up.**

**The Six will be back in a little while. They've wrapped up Season 5 right now and with some magic from the humans who take the credit, it will be released soon. God I wish it can come faster. HURRY UP HASBRO!**

**Disclaimer: I is not Hasbro nor BBC. I don't own Doctor Who and/or MLP:FiM.**

**ONWARDS!**

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><p>The wolf sat in front of the TARDIS, taunting the Doctor. She was licking her paw and flicking her tail around, frightening the ponies around her. Celestia and Luna were frozen in fear, but the Doctor was as calm as he could be. He walked down the carpet from the throne to the wolf's face. She stopped licking her paw and flicked her tail. The cloister bells inside the TARDIS ceased and the red light faded. The doors closed and the Doctor smiled. "BAD WOLF."<p>

_Doctor, it is good to see you once again. My my, it has been a while,_ she said.

"Yes, I remember. The Time War above the Earth was the last time, wasn't it?"

_I remember Davros's attempted destruction of the Multi-verse. Those were the good days though, weren't they?_

The Doctor grimaced. "I don't like to remember."

The BAD WOLF smiled. _You don't have a choice._

Behind him, Princess Celestia screamed out. "GUARDS!"

Behind the TARDIS, armored Pegasi and Unicorns charged at the BAD WOLF with spears. Earth Pony guards appeared from the two exists near the thrones and charged with armored helmets. The Doctor looked around with eyes wide. "No, DON'T!"

It was too late. Once the armed ponies got close, the BAD WOLF's eyes glowed gold and their spears turned to snakes. The armed ponies dropped the snakes immediately. The Earth Pony guards' helmets turned into pillows. They hit the BAD WOLF, but the only thing that happened was the room being filled with pillows. Twilight's jaw hung by the display of magic. The wolf's magic originated from her eyes, not the horn.

The wolf smiled. _Looks like my powers still work in this Universe. Fantastic,_ she said.

The Doctor sighed. "Why are you here?"

_I'm just passing through. I have to return to your Universe to gather the last component to the problem at hand. Although, I'm sure I can obtain what I need here._

It took the Doctor a moment to think about it. His eyes widened. "You don't mean—"

_The Doctor must return to the Universe. We need you Doctor_.

The Doctor laughed. "Oh no. No way is that happening. I'm no longer needed in that Universe. I regenerated. My future self is running around in that Universe—"

_And he needs your help._

Celestia's heart quickened. _There is a fluxuation in time. An event that can still go in any direction. An event you want to repeat and this time, you have a third choice._

The room was silent. _Gallifrey._

The fires in the Doctor's eyes raged. Ditzy walked over to the Doctor with concern in her eyes. "Doctor? Are you alright?"

He said nothing. "Doctor? Please say you're alright."

"But it's gone. I destroyed Gallifrey in order to stop the Time War. There cannot be a fluxuation in that particular event. It's a part of my time stream. Interfering in the Time War again would result in me crossing my own time stream. I cannot do that, unless I want the Universe to burn. Besides, there can't be a third choice," he said with a cracked voice.

_Ah, but that is the beauty of being the only Time Lord in existence. It is your words that define the laws of Time and Space. You can cross your own time stream by your word._

"No I can't! Besides, if I could, the war is Time Locked. I won't be able to intervene due to my people's own decision to lock the war. I cannot break the lock."

The BAD WOLF smiled. _It can be done. I've seen it. Gallifrey escaped the Time Lock before, thanks to Lord President and the Master. The Lock was broken by you when you decided to join the fighting. The Lock can be broken."_

"But I can't do it alone! I had help, I had resources!"

The wolf's eyes glowed. _Dear Doctor, you regret the decision you made all those years ago, don't you?_

The Time Lord sighed and nodded. _Then you know that somewhere deep down, you had a way to escape it. Either the Universe burns or Gallifrey falls. It is decisions like this that haunt many people and ponies. Princess Celestia faced that fact when Nightmare rose from the dark._

Celestia bowed her head in sadness. _You faced this decision on Gallifrey, and you chose the same choice Celestia made. For the good of the masses, you chose to cut your heart out. Now, you have a chance to heal. I can send you back to Gallifrey. You can save it. Gallifrey falls no more._

Those words rang out to those who understood what the BAD WOLF was talking about. Twilight's heart pretty much stopped. If what the wolf was saying is true, then the Doctor can heal from his pain. When he talked about crossing his own time stream, however, it made her think back to when she used Starswirl's Time Spell to tell herself not to worry about the following week (which failed). Perhaps telling that to the Doctor would be a bad idea.

Celestia looked over at her sister, who was taking in what the wolf was talking about. Celestia really did have no other choice but to banish Nightmare to the moon, even if she lost her sister in the process. She went over and hugged the princess of the Moon, who returned the display of kindness.

The wolf breathed in. _If you wish to save Gallifrey, then you will come with me. While you may accept, I must warn you that you cannot fly off still in a pony body._

The Doctor laughed. He would meet his future incarnation as a pony while the other would question his sanity, again. "You have a point there. I suppose I can go back and change everything."

_I am happy you made that decision. _With that, the BAD WOLF smiled and her eyes started to glow once again. This time, the Doctor's body began to glow like he was regenerating. The flames erupted, but they were gentle this time. The Mane 6 shielded themselves from the fires of the Doctor's transformation.

The flames died down, and in front of the whole of Equestria was not the same brown stallion as before. The creature in front of them was very tall and pink. The creature had enlarged forehooves that had strange digits at the ends of them. His brown fur was replaced by a brown long coat. Underneath the coat was a brown suit and tie with an hourglass tie pin attached to it. The creature's face was long and narrow. His snout was smaller and his mane was on top of his head. It was still as messy as before.

The creature looked down at the digits before him. He smiled as he reached into his coat and pulled out his Sonic Screwdriver. With a quick buzz at the crowd, the Doctor was back.

Ditzy flew up to the Doctor's new face. Instead of keeping her space, the pegasus hugged the Time Lord. The Doctor hugged back. "Oh it's so good to look like a Time Lord again!"

Princess Celestia smiled. "What's wrong with looking like a pony?"

"Well, I grabbed everything with my teeth and probably contracted several diseases, my fear of appearing everywhere in the buff is gone, and I can now grab things like I did before. Oh it feels so good to be back!" the Doctor said.

The princesses chuckled. The TARDIS grew to accommodate his new size. The BAD WOLF smiled up at the Time Lord. _I must say, I missed this form. And now, dear Doctor, it is time. Gallifrey awaits._

The Doctor nodded and kneeled down in front of his friends. "Alright, looks like I'm going away for a little while. Ditzy, take good care of yourself. Celestia, I expect you to be better at chess when I get back, and you Luna—"

He pointed at the alicorn "—we got a rematch coming up. Be ready."

The princess of the Night smiled. "Fighting is Magic is my territory, dear Doctor. I'm afraid I must ask you to improve your skills."

The Doctor laughed. "We'll see." He turned to the Mane 6. "It's been a pleasure working with all of you. We made a pretty good team, didn't we?"

The girls all agreed. Pinkie smiled and wiped a tear from a hanky pulled from Rarity's dress. "We'll miss ya Doctor!"

Rarity looked over. "Pinkie, that goes on my dress!"

"Sorry, I'll put it back."

"Egh, just keep it. It looked rubbish anyway," she said.

The Doctor cracked a smile. While Twilight joined in on the little conversation with Rarity, the Doctor eyed Applejack. With a silent nod, the message was clear. _Stay strong_. The farm pony nodded in a response and looked back at Twilight. She was going to have a rough next few years.

The Doctor turned to the BAD WOLF, who had the doors of the TARDIS opened. _I've created a pathway to our Universe, Doctor. Once you have completed your mission, you can use the same route to return._

He smiled and walked toward the TARDIS. Just before he entered, he turned around to face his friends again. He chuckled as he looked back up at the TARDIS. "Well then, enjoy the celebration! I remember it well. Oh, and lay off the confetti cannons unless you want the fountain to be filled with surprised ponies."

That warning was directed at Pinkie Pie. The Doctor smiled. "Well then, Allons-y!"

He closed the doors of the TARDIS. Immediately the engines started to kick up as the wonderful machine began to vanish from the Equestrian throne room. After a few moments, the TARDIS was completely gone, leaving the guards to deal with the snakes that were rudely turned by the BAD WOLF and the graffiti gone from the walls.

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><p>The Doctor flipped a few switches on the console as the TARDIS flew safely between dimensions. He couldn't stop looking at his hands as he worked in his wonderful machine. In his mind, he replayed how he would save Gallifrey and what his future self looked like. If he looks like a dork, he was going to lose it. Well, maybe if he was ginger, he wouldn't mind as much.<p>

As he continued to work with the TARDIS, the BAD WOLF stood nearby. She raised her paw at the Doctor's head. _You won't be going directly to Gallifrey._

The Doctor stopped what he was doing. _Her Majesty, Queen Elizabeth I needs your help. A group of Zygons have invaded England and are attempting to take control of the planet. You must travel to 1562 and snuff out the Zygons. It is there where your mission begins. You will also have no memory of you ever living in Equestria. Your last memory will be your journey to Mars after Davros's plot. Best of luck is wished upon you, Doctor._

The BAD WOLF lowered her paw. The Doctor shook his head and continued working at the console. With no more items on her agenda, except one more visit, the BAD WOLF vanished.


	25. Epilogue

**A/N: Well everyone, this is the last chapter of **_**Dark Vengeance. **_**It has been a great time writing this story for all of you. I hope you remember that I will still be around to pump out more stories and one-shots for the future. I will miss you all on this site. It's been great working for all of you. Remember if you want updates on my newer stories, follow me on Twitter at sir_scribe. I'll update **_**New Life in Ponyville,**_** but that will be it. Until the last update on this site. I'm SirScribe, or Scribe Featherhart, and it's been an honor.**

**Pinkie: PARTY!**

**Me: Ow, why?**

**Pinkie: It's the 127****th**** anniversary of Ponyville's founding and there is a big party in the Towne Square!**

**Applejack: It's a big party Scribe. Gonna need ya to work double time with them apples**

**Me: Gotcha boss. Anyway, let's get this wrapped up. I don't own MLP:FiM. All rights go to Hasbro.**

**Twilight: It will be a great way to get my mind off some things**

**Me: The party? Yeah, it's going to be fun.**

**Rainbow Dash: Well hurry up with the chapter!**

**Rarity: Rainbow Dash, you must not rush an author with his or her work. If you want a perfect ending to a story, you need patience and serenity.**

**Rainbow Dash: Have you met me? I don't have time for this!**

**Fluttershy: Um, Rainbow, can you please keep it down? If that's OK with you**

**Rainbow: Calm? I can't be calm when the line for the apple cider is growing!**

**Me: *facehoof* I have some cider in the fridge. Anyway, let's go**

**ONWARDS!**

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><p>Ditzy smiled as the dream returned to her. She was sitting on top of a cliff, overlooking a magnificent sunrise over an alien planet. The planet she was on was Bermuda 15, the beach planet. The planet is said to have sunrises that could melt the hearts of anypony who watched it. The planet was also the planet where the Doctor helped stop an infestation of the Black Demon virus, a virus that turned ponies into hallow shells of pure evil. Ditzy was lucky to have stumbled across the antidote when the Doctor fell ill. That was a good Tuesday.<p>

As the sun rose above the horizon, she could feel the Doctor sitting next to her. "Well, off on another adventure?"

Ditzy sighed as she looked over at him. She didn't have the familiar shine in her eyes whenever he asked that. In fact, in her eyes was confusion. Not about the question, but about her future as a citizen of a little planet tens of millions of light years away from there. She felt herself slip off the cliff and into the water. The Doctor shrieked and jumped in after her.

Ditzy felt herself sink to the bottom. She saw the Doctor break into the surface of the ocean and saw him swim to her. He was inches away from her hoof when she knocked it away. His hoof turned into smoke as his image faded into the water. The ocean was weighing down on Ditzy's chest, but she welcomed the pain. She felt herself softly land on the ocean floor. The darkness had enveloped her completely. She felt the eyes of sea creatures around her.

The wall-eyed pegasus looked around at her surroundings. Indeed, sea creatures of every size and species came to see her. Some looked fearsome while others looked at her with confusion. One of the sea creatures approached her with hesitation. She held her arms out as the creature came between them. They both shared a hug under the sea.

Ditzy's eyes shot open. Her eyes readjusted as she looked around her. She felt her breathing labored and her chest heavy. She was on her bed and in her room. It was night with a full moon. Ever since the Doctor disappeared, Ponyville had its share of unusual happenings. The Everfree Forest attacked the city and the bearers of the Elements were powerless. The Forest had retreated, but the Mane 6 returned with no jewels.

When the trials for the Equestria Games came in, she was put on the Ponyville team to replace Rainbow Dash while she was injured. Of course, she immediately recovered, but she didn't mind. She was still there when the games began. The peaceful scene of Equestria had ceased after the sudden attack against the princesses a while ago.

Ditzy's ear twitched at a faint sound growing in the distance. She hopped out of her bed and ran to the window. There was the magical blue box that she remembered so well. She quickly flew down the stairs and threw up the door. Of course, there was the Doctor with his blue suit vest and tie. He didn't look a day older than when he left. His usual grin greeted the pegasus. "Doctor, you're back!"

"And it's good to be back. I've got to say, it took me a while to get the hang of my hands and feet again," he said.

"You mean those weird things that other weird thing gave you?"

He nodded and chuckled. "Anyway, I'm back for you. We still have a whole Universe to explore, and more bad guys to stop. What do you say, wanna come back to the TARDIS?"

Ditzy's face turned red with embarrassment. The Doctor was quick to notice. With no more words, she walked into the house and motioned the Doctor to follow.

The Doctor sighed as he entered the room. The room was just big enough for a filly, and sure enough, there was a young unicorn sleeping in the bed. An old music box was playing in the background, probably what lulled the filly to sleep in the first place. The Doctor wanted to curl up and sleep as well with the music playing, but he knew that wasn't going to happen. He was a Time Lord who spent almost a millennia running. He wasn't tired.

"How long was I gone?"

"2 years Doctor. I found her a while ago and Carrot Top helped me raise her. I wanna be there for her Doctor, so I am retiring from the TARDIS," Ditzy said.

The Doctor smiled. "You remind me of the nanny we met on Mal-Relati. I understand Derpy, and I imagine that these past few months have been tough on you," he said.

Ditzy nodded. "So many things happened Doctor, but I want Dinky to be safe."

"Oh so her name is Dinky?"

Ditzy smiled. She yawned as she closed the door. "I wanna get some sleep Doctor, you don't mind, do you?"

The Doctor only smiled. "Has my derpy best friend finally grown up?"

She smiled and shook her head. "Nope, I'm still me. I accidentally almost crashed into Rainbow Dash's house the other day. I ended up crashing into Twilight's castle though, but she wasn't home," she said.

The Doctor sighed. On the way inside, he did notice a bigger tree where Twilight's library was. He wondered if she expanded the Treehouse. The Doctor waved goodbye to Ditzy and left the house, leaving Ditzy to her daughter's bedroom door. As she turned in the opposite direction of the Doctor, she could hear the sound of the engines firing up. She shut her eyes and focused on the sound of the TARDIS. She implanted the sound into her memory before heading back into bed. That would be the last time she would be inside the TARDIS. She didn't count on the fact that she would see the Doctor again, but it would be under a different set of circumstances. Circumstances that would bring the Doctor back from the end of time.

* * *

><p>Applejack was sound asleep when she heard the TARDIS engines.<p>

Even though it had been a year and a half since Tirek unleashed pure chaos in Equestria, Applejack still had nightmares from that day. She would scream at night, trying to fight off Tirek as she tried sucking every ounce of her life force away. Her nightmares always started after Twilight surrendered to the demonic centaur. Discord would still be trapped and without the last key, they were doomed. Applejack remembered that day, and the events following it.

Apple Bloom and her friends were lucky to have been camping with Zecora when Tirek was free. Fearing their safety, Applejack sent the CMC away in order to deal with the problem. Her plan worked, and telling her young sister about what had happened was bad enough.

She was in the middle of the field, and Tirek hoisted her up to his eye level. Applejack was petrified, and right as he began extracting her life force, the sounds of a whirring engine erupted. The dream Tirek and Applejack turned to the sound of the noise. Materializing on the field was a small blue box. Tirek released Applejack and approached the box. A brown stallion emerged from the box and calmly walked up to the cloven hoof of Tirek.

The stallion looked up and chuckled. "I've seen worse than you! Ponies have nightmares of you, but you will soon be having nightmares of me!" he said.

Applejack smiled. She looked up and noticed a hole burning in Tirek's chest as the stallion continued to stare into his soul. An explosion erupted behind her, and she saw herself and the rest of the Mane 6 with their new magical forms. They cast a spell on Tirek, destroying his power. Applejack smiled as she remembered that moment.

The cowpony ran to the Doctor and threw a big hug on him. He chuckled and returned the hug. Before she could say anything, the Doctor whispered in her ear: "Wake up."

Applejack sat straight up in her bed. She looked around her room. Nopony was there. She wiped the sweat off her forehead and proceeded back to sleep, but she heard the sounds of a rusty, whirring machine coming from outside. She recognized that sound immediately. She looked out her window. Outside the farm, the Doctor's TARDIS was materializing at the edge of the Everfree. She smiled as she grabbed her Stetson and bolted out the door.

She snuck out of the barnhouse and ran through the fields. When she reached the border between her farm and the Everfree, she stopped. It was really the TARDIS, and coming out of it was the Doctor. He seemed to have been stumbling as he closed the door behind him. Applejack chuckled as she jumped over the fence.

"Ah never thought ah would see ya again," she said.

The Doctor spun around. Apparently he was facing the Forest. "I come back from time to time. Sometimes not with this face," he said.

Applejack chuckled. "Ya have been gone fer 2 years now, Doctor. That was a mighty big job ya had to do back in yer Universe."

"I'm a time traveler, I can't measure time outside while traveling. It could've been 2 years or 2 seconds. It's good to see some things haven't changed," he said, looking at the barn.

Applejack spun around. "Twilight got a new library, Rainbow made it to the Wonderbolts, and ah am the owner of Sweet Apple Acres."

The Doctor smiled. "It's good to know I'm on track with history."

Applejack smiled. "So ya'll off on more adventures with yer friend?"

"No, she has something more important to do. It's fine, really. She is needed here in Ponyville for Dinky, so I can understand that she wants to leave," the Doctor said.

"Ah know how ya mean. Twilight is traveling again and most of us got our own lives again," she said.

The Doctor nodded. "This won't be the end of her travels. If I know my Equestrian history, Twilight does a lot of digging into Luna's maps of the Universe. Of course she is going to be traveling, although, I think I have said too much."

Applejack sighed. "Anyway, I'd best be moving on. Planets to see, ponies to save, bets to pay, all that stuff. I owe Cadence's father a few chickens for a bet I made," the Doctor said.

"What was the bet?"

"Doesn't matter, unless you would want to…"

Applejack stared at him. "…want to come with me."

The farm pony looked over at the TARDIS. "Go with yew, inside the TARDIS?"

The Doctor shrugged. "Yeah why not? It's going to be fun."

"All that stuff that happened all those years ago, all that was nuthin' to ya?"

"Just a regular day for me. I don't mind sharing that normal day with you though. What do you say: want to come with me?"

Applejack thought about it for a moment. "Ah have mah family to look for. Ah don't have the time to leave."

"But that's the thing with the TARDIS. You can come with me and you can be back within a few hours. Nopony will ever know you left," the Doctor said. "The beauty of time travel."

Applejack looked over at the TARDIS again. She remembered what it was like in the TARDIS when they were invading Sombra's Stronghold inside Canterlot. The rooms she entered were amazing, but she knew that there were so many more than just a few rooms. "Anywhere in time and space?"

"Anytime and place. The past, present, and future are yours to visit. We can visit your great-grandparents back when they stumbled upon the Big Macintosh apple. We can go to Twilight's wedding, we can travel with Princess Twilight's 'Cosmic Exploration' program. We can have tea with Celestia and her mother, we can go anywhere and meet anypony. The only thing stopping you from seeing it all is this decision," he said.

Applejack turned to the Doctor. She fixed her Stetson and smiled. "Ah'm in," she said.

The Doctor smiled and led her into the TARDIS. The interior looked cleaner, like he put an effort into fixing it up a bit. The Doctor closed the door behind him and followed the cowpony into the control room. Applejack ran a hoof on the console. The last time she saw this was on their victory day. She remembered her friends running around with everything they needed to storm Canterlot. She remembered seeing the ground forces direct from Ponyville anxious to get inside the royal city.

The Doctor released the brake and looked over to Applejack. "So, where do you want to start?"

Applejack thought about it for a moment before she smiled. "Ah want to make a pit stop before we go. Ah need to get mah stuff first."

The Doctor nodded and watched Applejack throw open the doors. She ran across the field and into her farmhouse. He watched her leave and pulled out a book from under the console. It was the book that Twilight used to discover the secret of the Elements. The book he shut on her. He turned to the bookmarked page and read to himself:

_Based on my earlier investigations, I have concluded that the Elements are alive. This theory had scared Luna a little bit, but at least I didn't divulge what else I uncovered to her and Princess Celestia. After doing some digging, I have discovered a fatal flaw in the Element's design. Instead of focusing mainly on good energy and magic, it has an open defense. A defense that can be penetrated by dark magic._

_I've tested my theory using dark magic. I must say, if King Sombra knew of the Elements and turned them, there wouldn't be a kingdom under the Sun. The Elements magnify one's magical arsenal and uses the magic of their choice to work. If the Elements were used with dark magic, what they would do would contradict their original purpose: to provide harmony and life. If they are turned, then they can wipe out all life in Equestria. If this comes to be, the Elements of Harmony will be no more._

_They will bring Armageddon. They will become the Elements of Disaster._

_-Starswirl the Bearded_

The Doctor sighed as he knew that this day would come. He remembered the prophecy he was told, especially the last two lines:

_**The kingdom of twilight will rise and then,**_

_**Mark Equestria's End**_

After a few minutes, she returned with a box strapped onto her back. The Doctor immediately hid the book under the console. With a destination from his companion, the TARDIS doors slammed shut and immediately dematerialized.

Trixie fidgeted in her nightmare. The two years she spent traveling across Equestria bore little fruit. Her wagon was paid off thanks to a grateful soul in Ponyville, her magic began expanding, and more ponies started noticing her. She could say it was amazing, but she always appeared AFTER princess Twilight. Twilight was the main event and Trixie was the shadow that followed. It didn't help with her magical hat being damaged in the war a few years back.

Ever since the changelings ruined her hat, she had a violent reaction every time one appeared before her. Each time she fought and beaten a changeling, she remembered the little voice in the back of her head screaming _'A wizard is nothing without a hat!' _Trixie had parked her wagon on a tree at the top of a hill. She was to perform at Trottingham in the next few days, and she was a month ahead of Twilight. She sighed in her empty wagon.

Suddenly, there came a knock on the door. Trixie heard it but didn't move. _Probably a prankster leaving a bag of unmentionables again,_ she thought to herself.

Another knock broke the silence. Trixie groaned as her dream ended and she was pulled back into reality. She looked up at the door. Another knock came in, and Trixie sighed. "Who dares disturb the Great and Powerful Trixie?!"

She heard a thud on the ground. There was one more knock, and the sound of a pony running away. Trixie sighed as she pulled out a brick from under her bed. She grabbed the door knob with her magic, and threw it open. She raised the brick to find that nopony was there. The night was still around and crickets chirped in the night. The only difference in that scene was a brown box sitting at her doorstep. She looked around, looking for the mailmare who delivered it. On the box was a note.

Trixie picked up the note. It read _A wizard is not without her hat._

'_Oh great, my nightmare is real,'_ she thought. She opened the box and caught her squeak. Inside was her hat fully patched up. She grabbed the hat with her magic and placed it on top of her head. Suddenly, she felt something sharp poking at her head. She raised the hat, and a metal rod fell out. It was a magic wand with another note on it.

'_Thank ya fer helpin' with Ponyville all them years ago. Try and not get ponies upset._

_-AJ'_

She smiled as she raised the wand. She looked around and still saw nothing. The only things on the hill was a tree, and…a blue box? The brightly lit box stood there, staring at her. She did not know why, but Trixie found herself waving at the box. She picked up the box and wand, and reentered her wagon. The last sound she heard before falling back to sleep was the sound of the engines of the TARDIS fading into the dark.

The End


End file.
